RNA Sequencing of the Human Milk Fat Layer Transcriptome Reveals Distinct Gene Expression Profiles at Three Stages of Lactation
2023-06-08
1 Introduction
Because of the numerous benefits breastfeeding provides, it’s recommended that infants be exclusively breastfed for the first 6 months with continued breastfeeding for at least 1 year. However lactation is not achieved in all mothers and the physiology of this process remains poorly understood. This is because of questions related to the ethics of performing tests or extracting tissues from lactating mother.
So, an interesting alternative has been proposed – human milk secreted during lactation is a rich source of mammary epithelial cell RNA. About 3–8% of human milk fat globules contain mammary epithelial cell cytoplasmic remnants, including RNA, captured during milk fat globule formation and secretion
Previous to this research, there has been attempt to undestand the human milk fat layer transcriptome with microarray techniques. This paper analyses the transcriptome with RNA-seq which, compared to microarray, has highly sensitive detail, can accurately quantify both very low and very high abundance transcripts, as well as detect novel transcripts.
The authors of this paper (Lemay et al. 2013), furthermore, suggest that the constitution of the human milk is not dependent on the days postpartum, which is the measure typically used by lactation researchers to categorize lactation stage. Rather, they state that compared to other factors such as subject, washing protocol, or time of collection, biochemically defined lactation stage (i.e., Na:K) has the largest effect on the transcriptome. So they categorise the samples as: “colostral” if Na:K >= 2.0; and as “transitional” if Na:K < 2.0; “mature” if Na:K < 0.6 .
The three main challanges of this paper are:
because of the sample extraction, it is unknown if the milk fat layer yields RNA purely of mammary epithelial cell origin, or if RNA from non-mammary epithelial sources is also present in the milk fat layer obtained from colostrum, transitional, or mature human milk,
because of the body heat and the environment of the milk, the RNA might end up being degraded (low RIN values),
because this is a study of patients who would agree to participate after just having gone through giving birth and have to fulfill some criteria, the sample size is very small which is something that really influences the information that can be extracted and extrapolated from this sample group - the result of bias of such a small sample group is really apparent in the MA-plots
2 Quality assessment
2.1 Data import and cleaning
We start importing the raw table of counts.
library(SummarizedExperiment)
se <- readRDS(file.path(system.file("extdata", package="IEOproject"), "GSE45669.rds"))
#se <- readRDS("../inst/extdata/GSE45669.rds")
se
class: RangedSummarizedExperiment
dim: 25118 16
metadata(4): experimentData annotation ensemblVersion urlProcessedData
assays(1): counts
rownames(25118): 1 10 ... 9994 9997
rowData names(5): gene_id gene_biotype description gene_id_version
symbol
colnames(16): SRR801690 SRR801691 ... SRR801704 SRR801705
colData names(37): title geo_accession ... lactation stage:ch1 subject
id:ch1We have 25118 genes by 16 samples. From the first row and column names shown by the object, we can figure out that genes are defined by Entrez (Maglott et al. 2010) identifiers and samples by Sequence Read Archive Run (SRR) identifiers.
Regarding the samples, we can see that tey are few, so the analysis results quality will be likely affected by this fact. It is important to keep it in mind along the process.
The row data in this object contains information about the profiled genes.
head(rowData(se))
DataFrame with 6 rows and 5 columns
gene_id gene_biotype description
<character> <character> <character>
1 ENSG00000121410 protein_coding alpha-1-B glycoprote..
10 ENSG00000156006 protein_coding N-acetyltransferase ..
100 ENSG00000196839 protein_coding adenosine deaminase ..
1000 ENSG00000170558 protein_coding cadherin 2 [Source:H..
10000 ENSG00000117020 protein_coding AKT serine/threonine..
100008586 ENSG00000236362 protein_coding G antigen 12F [Sourc..
gene_id_version symbol
<character> <character>
1 ENSG00000121410.11 A1BG
10 ENSG00000156006.4 NAT2
100 ENSG00000196839.12 ADA
1000 ENSG00000170558.8 CDH2
10000 ENSG00000117020.16 AKT3
100008586 ENSG00000236362.8 GAGE12FAmong this information, the gene symbol and description are potentially useful for interpreting results of, for instance, a differential expression analysis. Let’s explore now the column (phenotypic) data.
dim(colData(se))
[1] 16 37
head(colData(se), n=3)
DataFrame with 3 rows and 37 columns
title geo_accession status submission_date
<character> <character> <character> <character>
SRR801690 154-D_RNA_c0_0 GSM1111646 Public on Jul 22 2013 Apr 01 2013
SRR801691 158-1_RNA_c0_0 GSM1111647 Public on Jul 22 2013 Apr 01 2013
SRR801692 160-J_RNA_c0_2 GSM1111648 Public on Jul 22 2013 Apr 01 2013
last_update_date type channel_count source_name_ch1
<character> <character> <character> <character>
SRR801690 May 15 2019 SRA 1 Milk Fat Layer
SRR801691 May 15 2019 SRA 1 Milk Fat Layer
SRR801692 May 15 2019 SRA 1 Milk Fat Layer
organism_ch1 characteristics_ch1 characteristics_ch1.1
<character> <character> <character>
SRR801690 Homo sapiens subject id: 154 lactation stage: Tra..
SRR801691 Homo sapiens subject id: 158 lactation stage: Tra..
SRR801692 Homo sapiens subject id: 160 lactation stage: Tra..
characteristics_ch1.2 molecule_ch1 extract_protocol_ch1
<character> <character> <character>
SRR801690 extraction protocol:.. polyA RNA Soft Spin: Whole mil..
SRR801691 extraction protocol:.. polyA RNA Soft Spin: Whole mil..
SRR801692 extraction protocol:.. polyA RNA Soft Spin: Whole mil..
extract_protocol_ch1.1 extract_protocol_ch1.2 extract_protocol_ch1.3
<character> <character> <character>
SRR801690 Hard Spin: Whole mil.. Wash: After a hard s.. RNA Isolation: Total..
SRR801691 Hard Spin: Whole mil.. Wash: After a hard s.. RNA Isolation: Total..
SRR801692 Hard Spin: Whole mil.. Wash: After a hard s.. RNA Isolation: Total..
extract_protocol_ch1.4 taxid_ch1 data_processing
<character> <character> <character>
SRR801690 RNA libraries were p.. 9606 Basecalls performed ..
SRR801691 RNA libraries were p.. 9606 Basecalls performed ..
SRR801692 RNA libraries were p.. 9606 Basecalls performed ..
data_processing.1 data_processing.2 data_processing.3
<character> <character> <character>
SRR801690 Reads mapped to the .. Mapped reads were in.. Normalized transcrip..
SRR801691 Reads mapped to the .. Mapped reads were in.. Normalized transcrip..
SRR801692 Reads mapped to the .. Mapped reads were in.. Normalized transcrip..
data_processing.4 data_processing.5 platform_id data_row_count
<character> <character> <character> <character>
SRR801690 Genome_build: hg19 Supplementary_files_.. GPL11154 0
SRR801691 Genome_build: hg19 Supplementary_files_.. GPL11154 0
SRR801692 Genome_build: hg19 Supplementary_files_.. GPL11154 0
instrument_model library_selection library_source library_strategy
<character> <character> <character> <character>
SRR801690 Illumina HiSeq 2000 cDNA transcriptomic RNA-Seq
SRR801691 Illumina HiSeq 2000 cDNA transcriptomic RNA-Seq
SRR801692 Illumina HiSeq 2000 cDNA transcriptomic RNA-Seq
relation relation.1 supplementary_file_1
<character> <character> <character>
SRR801690 SRA: https://www.ncb.. BioSample: https://w.. NONE
SRR801691 SRA: https://www.ncb.. BioSample: https://w.. NONE
SRR801692 SRA: https://www.ncb.. BioSample: https://w.. NONE
extraction protocol:ch1 lactation stage:ch1 subject id:ch1
<character> <character> <character>
SRR801690 Soft spin, Unwashed Transitional 154
SRR801691 Hard spin, Unwashed Transitional 158
SRR801692 Hard spin, Washed once Transitional 160We have a total of 37 phenotypic variables. The
second column geo_accession contains GEO Sample Accession Number
(GSM) identifiers.
GSM identifiers define individual samples, understood in our context as
individual sources of RNA. In this dataset, there are no technical replicates.
To proceed further exploring this dataset, we are going to use the
edgeR package and build a
DGEList object, incorporating the gene metadata, which includes the
gene symbol.
library(IEOproject)
library(edgeR)
dge <- DGEList(counts=assays(se)$counts, genes=rowData(se))
dim(dge)
[1] 25118 16Calculate \(\log_2\) CPM units of expression and put them as an additional assay element to ease their manipulation.
assays(se)$logCPM <- cpm(dge, log=TRUE, prior.count=0.25)
assays(se)$logCPM[1:5, 1:5]
SRR801690 SRR801691 SRR801692 SRR801693 SRR801694
1 -7.2388751 -7.2388751 -4.648112 -3.248656 -7.2388751
10 -4.3144409 -2.1092005 -7.238875 -7.238875 -0.8796359
100 2.1843310 -0.7364584 2.080955 2.589905 0.7185524
1000 -7.2388751 -7.2388751 -7.238875 -7.238875 -0.9566625
10000 -0.5045971 -3.4982615 -1.559628 4.905827 -0.9566625In the codeblock below, we loop through all the columns of the phenotype table to see if there are any variables for which there are groups (batch-effect):
# loop over the columns and count unique values
for (col in names(colData(se))) {
unique_vals <- unique(colData(se)[[col]])
if (any(length(unique_vals) %in% c(1, 16))) {
next # skip to the next column
} else {
counts <- table(colData(se)[[col]])
cat(paste0("Column '", col, "' has ", length(unique_vals), " unique values:\n"))
print(counts)
}
}
Column 'characteristics_ch1' has 11 unique values:
subject id: 153 subject id: 154 subject id: 158 subject id: 160 subject id: 168
1 1 1 1 1
subject id: 174 subject id: 179 subject id: 183 subject id: 187 subject id: 188
1 3 3 2 1
subject id: 359
1
Column 'characteristics_ch1.1' has 3 unique values:
lactation stage: Colostrum lactation stage: Mature
3 8
lactation stage: Transitional
5
Column 'characteristics_ch1.2' has 4 unique values:
extraction protocol: Hard spin, Unwashed
5
extraction protocol: Hard spin, Washed once
6
extraction protocol: Hard spin, Washed twice
3
extraction protocol: Soft spin, Unwashed
2
Column 'extraction protocol:ch1' has 4 unique values:
Hard spin, Unwashed Hard spin, Washed once Hard spin, Washed twice
5 6 3
Soft spin, Unwashed
2
Column 'lactation stage:ch1' has 3 unique values:
Colostrum Mature Transitional
3 8 5
Column 'subject id:ch1' has 11 unique values:
153 154 158 160 168 174 179 183 187 188 359
1 1 1 1 1 1 3 3 2 1 1 In the output above we can observe the columns containing groups of data values, that means excluding the columns presenting the same value for all samples or a different value for each sample. We can see that there are:
patients that are repeated because their milk was sampled in 2 or 3 of the 3 stages of lactation reported in the paper (id numbers: 179, 183, 187).
given the different 3 stages, 3 groups of samples appear (this is a biologically relevant factor): Colostrum lactation stage; Mature lactation stage; Transitional lactation stage.
because of the different protocols there are 4 different groups (technically relevant) Hard spin, Unwashed ; Hard spin, Washed once ; Hard spin, Washed twice ; Soft spin, Unwashed.
To facilitate handling these variables we are going to recode them as follows.
First we replace spaces in column names.
# simpler names
names(colData(se))[37] <- "id"
names(colData(se))[36] <- "lacStage"
names(colData(se))[35] <- "protocol"
# creating factors
colData(se)$idFac <- factor(colData(se)$id)
# colData(se)$lacStageFac <- factor(colData(se)$lacStage)
colData(se)$lacStageFac <- factor(colData(se)$lacStage,
levels = c("Colostrum", "Transitional", "Mature"),
labels = c(1, 2, 3))
#colData(se)$protocolFac <- factor(colData(se)$protocol)
colData(se)$protocolFac <- factor(colData(se)$protocol,
levels = c("Soft spin, Unwashed", "Hard spin, Unwashed", "Hard spin, Washed once", "Hard spin, Washed twice"),
labels = c(1, 2, 3, 4 ))In Table 1 below, we show this variable jointly with lactation stage and protocol to try to gather as much understanding as possible on the underlying experimental design.
| Patient | lacStage | protocol |
|---|---|---|
| 154 | Transitional | Soft spin, Unwashed |
| 158 | Transitional | Hard spin, Unwashed |
| 160 | Transitional | Hard spin, Washed once |
| 187 | Colostrum | Hard spin, Unwashed |
| 179 | Transitional | Hard spin, Washed once |
| 183 | Colostrum | Hard spin, Washed once |
| 187 | Colostrum | Hard spin, Washed once |
| 188 | Transitional | Hard spin, Washed once |
| 179 | Mature | Hard spin, Unwashed |
| 183 | Mature | Hard spin, Unwashed |
| 168 | Mature | Hard spin, Washed twice |
| 359 | Mature | Soft spin, Unwashed |
| 179 | Mature | Hard spin, Washed twice |
| 183 | Mature | Hard spin, Washed twice |
| 174 | Mature | Hard spin, Washed once |
| 153 | Mature | Hard spin, Unwashed |
2.2 Sequencing depth
Let’s examine the sequencing depth in terms of total number of sequence read counts mapped to the genome per sample. The figure below shows the sequencing depth per sample, also known as library sizes, in increasing order.
From the plot above we don’t notice any biases related to the different lactation stages (colors). The only thing that stands out is SRR801705 as having very low sequencing depth. In the later part of the analysis we will remove it from the analysis, since it seems to be an error with the sample sequencing.
From the plot above we do not see any bias. The “Hard spin, Washed once” groups together but there doesn’t seem to be a significantly extreme difference in their sequencing depth. We will further analyze this with a clustering approach.
2.3 Distribution of expression levels among samples
Figure 1 below shows the distribution of expression values per sample in logarithmic CPM units of expression.
Figure 1: Non-parametric density distribution of expression profiles per sample
There are no substantial differences between the samples in the distribution of expression values.
par(mar=c(7, 5, 2, 2))
boxplot(assays(se)$logCPM, col="gray", ylab=expression(log[2] * "CPM"),
cex.axis=1.2, cex.lab=1.5, las=2)
In the previous plots we see that the SRR801705 sample does not behave differently than the rest, but this is due to the fact that we are now considering the counts per million (CPM), and what is wrong about that sample is the sequencing depth, so still we will exclude it from the analysis.
2.4 Distribution of expression levels among genes
Let’s calculate now the average expression per gene through all the samples. Figure 2 shows the distribution of those values across genes.
Figure 2: Distribution of average expression level per gene
As expected, we have two modes, one for genes that are lowly expressed in nearly all samples and another for genes with some detectable levels of expression across a number of samples.
2.5 Filtering of lowly-expressed genes
In the paper, transcript abundances were estimated as FPKMs (fragments per kilobase of exon per million fragments mapped) using Cufflinks. Genes with a mean expression level less than 0.01 FPKM (manually set) across all time points and all samples were excluded from further analysis.
In our analysis, we use CPM (counts per million) and after some trial and error we found that the best cutoff value from the cpm would be arround 0.1.
#cpmcutoff <- round(10/min(dge_sample_filtered$sample$lib.size/1e6), digits=1)
cpmcutoff <- 0.1
print(cpmcutoff)
[1] 0.1
#nsamplescutoff <- min(table(se_sample_filtered$protocolFac))
nsamplescutoff<- 15
print(nsamplescutoff)
[1] 15
mask <- rowSums(cpm(dge_sample_filtered) > cpmcutoff) >= nsamplescutoff
se.filt <- se_sample_filtered[mask, ]
dim(se.filt)
[1] 11729 15
dge.filt <- dge_sample_filtered[mask, ]
dim(dge.filt)
[1] 11729 15
par(mar=c(4, 5, 1, 1))
h <- hist(avgexp, xlab=expression("Expression level (" * log[2] * "CPM)"),
main="", las=1, col="grey", cex.axis=0.95, cex.lab=1.2)
x <- cut(rowMeans(assays(se.filt)$logCPM), breaks=h$breaks)
lines(h$mids, table(x), type="h", lwd=10, lend=1, col="darkred")
legend("topright", c("All genes", "Filtered genes"), fill=c("grey", "darkred"))
We are left with 11729 genes.
2.6 Normalization
We calculate now the normalization factors on the filtered expression data set.
dge.filt <- calcNormFactors(dge.filt)Replace the raw log2 CPM units in the corresponding assay element of the
SummarizedExperiment object, by the normalized ones.
assays(se.filt)$logCPM <- cpm(dge.filt, log=TRUE,
normalized.lib.sizes=TRUE)2.7 MA-plots
We examine now the MA-plots of the normalized expression profiles in Figure 3.
Figure 3: MA-plots of filtered and normalized expression values
A number of samples display some expression-level dependent bias. For cases in which this occurs at the low-end of the expression level, one solution could be to have a more stringent filter on minimum expression using a grouping with more samples per group, for instance. However, considering the low number of samples we are working with we decide to keep it this way. Of course, we should keep an eye on samples with these biases in case they also display other unexpected features, because then we might consider removing them.
2.8 Experimental design and batch identification
Here try to understand the underlying experimental design. We take a look at the combination of sample preparation protocol and lactation stage.
table(se.filt$lacStageFac, se.filt$protocolFac)
1 2 3 4
1 0 1 2 0
2 1 1 3 0
3 1 2 1 3We can see that not all the protocols have been used in all lactation stages, but still the distribution is quite balanced and the number of missing combinations is not critical for the analysis. This means that there are more chances that the differences observed are due to biological reasons rather than technical.
We examine now how samples group together by hierarchical clustering and multidimensional scaling, annotating lactation stage (number) and protocol(color) for each sample. We calculate again log CPM values with a high prior count(3) to moderate extreme fold-changes produced by low counts. The resulting dendrogram is shown in Figure 4.
Figure 4: Figure S6: Hierarchical clustering of the samples
Labels correspond to treatment and sample identifer, while colors indicate sample group.
We can see that the samples do not seem to group by protocol. Now we will test if they group by lactation stage in the figure below.
(#fig:sampleClustering_1)Hierarchical clustering of the samples. Labels correspond to treatment and sample identifer, while colors indicate sample group.
We can clearly see that the samples group by lactation stage in the clustering, since each cluster contains samples from a lactation stage, with the only exception of the sample SRR801691.
Next we will perform an MDS plot using the names of the lactation stages and colors according to protocol in order to ratify if they in deed group by lactation stage (Figure 5).
Figure 5: Figure S7: Multidimensional scaling plot of the samples
Labels correspond to treatment and colors indicate sample group.
In fact, the samples group by lactation stage.
3 adsasdassadffsa
Col_exp <- rowMeans(logCPM[, se_sample_filtered$lacStage=="Colostrum"])
Tra_exp <- rowMeans(logCPM[, se_sample_filtered$lacStage=="Transitional"])
Mat_exp <- rowMeans(logCPM[, se_sample_filtered$lacStage=="Mature"])plot((Tra_exp+Col_exp)/2, Tra_exp-Col_exp, pch=".", cex=4, las=1)
plot((Mat_exp+Col_exp)/2, Mat_exp-Col_exp, pch=".", cex=4, las=1)
plot((Mat_exp+Tra_exp)/2, Mat_exp-Tra_exp, pch=".", cex=4, las=1)
4 Differential expression
We now perform an analysis to observe differential expressed (DE) genes by excluding each of the 3 lactation stages one by one. This is also the approach that is described in the paper.
First, we will observed stage 1 and 2 that correspond to colostrum and transitional stage, leaving out the maturation stage (stage 3). Afterwards, we will exclud colostrum stage (stage 1) and finally we will exclud transitional stage (stage 2).
library(sva)4.1 Between Colostrum and Transitional
Checking the distribution of differentially expressed genes:
se.filt.all <- se.filt[,se.filt$lacStageFac!=3]
se.filt.all$stage <- droplevels(se.filt.all$lacStageFac)
mod <- model.matrix(~ se.filt.all$stage,
colData(se.filt.all))
mod0 <- model.matrix(~ 1, colData(se.filt.all))
pv <- f.pvalue(assays(se.filt.all)$logCPM, mod, mod0)
hist(pv, main="", las=1)
mask <- p.adjust(pv, method="fdr") < 0.1
DEgenesEGs <- names(pv)[mask]
DEgenesSyms <- mcols(se.filt)[DEgenesEGs, "symbol"]
DEgenesPvalue <- pv[mask]
DEgenesDesc <- mcols(se.filt)[DEgenesEGs, "description"]
DEgenesDesc <- sub(" \\[.+\\]", "", DEgenesDesc)
DEgenesTab <- data.frame(EntrezID=DEgenesEGs,
Symbol=DEgenesSyms,
Description=DEgenesDesc,
"P value"=DEgenesPvalue,
stringsAsFactors=FALSE, check.names=FALSE)
DEgenesTab <- DEgenesTab[order(DEgenesTab[["P value"]]), ] ## order by p-value
# rownames(DEgenesTab) <- 1:nrow(DEgenesTab)4.1.1 for volcano
sv <- sva(assays(se.filt.all)$logCPM, mod=mod, mod0=mod0)
Number of significant surrogate variables is: 3
Iteration (out of 5 ):1 2 3 4 5
mod <- cbind(mod, sv$sv)
colnames(mod) <- c(colnames(mod)[1:2], paste0("SV", 1:sv$n))
fit3 <- lmFit(assays(se.filt.all)$logCPM, mod)
fit3 <- eBayes(fit3)
tt3 <- topTable(fit3, coef=2, n=Inf)
DEgenes_no3 <- rownames(tt3)[tt3$adj.P.Val < 0.1]
sort(table(tt3[DEgenes_no3, "chr"]), decreasing=TRUE)
integer(0)
res3 <- decideTests(fit3, p.value=0.1)
genesmd <- data.frame(chr=as.character(seqnames(rowRanges(se.filt.all))), symbol=rowData(se.filt.all)[, 5], stringsAsFactors=FALSE)
fit3$genes <- genesmd
volcanoplot(fit3, coef=2, highlight=7, names=fit3$genes$symbol, main="Known+Unknown covariates", las=1)
mask <- DEgenesTab$EntrezID %in% DEgenes_no3
DEgenesTab <- DEgenesTab[mask,]In the table 2 the DE genes with lowest p-values are displayed:
| EntrezID | Symbol | Description | P value | |
|---|---|---|---|---|
| 10672 | 10672 | GNA13 | G protein subunit alpha 13 | 0e+00 |
| 116985 | 116985 | ARAP1 | ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 | 1e-07 |
| 144110 | 144110 | TMEM86A | transmembrane protein 86A | 1e-07 |
| 391 | 391 | RHOG | ras homolog family member G | 1e-07 |
| 1200 | 1200 | TPP1 | tripeptidyl peptidase 1 | 1e-07 |
| 54978 | 54978 | SLC35F6 | solute carrier family 35 member F6 | 1e-07 |
| 155400 | 155400 | NSUN5P1 | NOP2/Sun RNA methyltransferase family member 5 pseudogene 1 | 1e-07 |
| 5538 | 5538 | PPT1 | palmitoyl-protein thioesterase 1 | 1e-07 |
| 4286 | 4286 | MITF | melanogenesis associated transcription factor | 1e-07 |
| 55604 | 55604 | CARMIL1 | capping protein regulator and myosin 1 linker 1 | 2e-07 |
4.2 Between Transitional and Mature
Checking the distribution of differentially expressed genes:
se.filt.all <- se.filt[,se.filt$lacStageFac!=1]
se.filt.all$stage <- droplevels(se.filt.all$lacStageFac)
mod <- model.matrix(~ se.filt.all$stage,
colData(se.filt.all))
mod0 <- model.matrix(~ 1, colData(se.filt.all))
pv <- f.pvalue(assays(se.filt.all)$logCPM, mod, mod0)
#sum(p.adjust(pv, method="fdr") < 0.05)
#sum(p.adjust(pv, method="fdr") < 0.1)
hist(pv, main="", las=1)
mask <- p.adjust(pv, method="fdr") < 0.1
DEgenesEGs <- names(pv)[mask]
DEgenesSyms <- mcols(se.filt)[DEgenesEGs, "symbol"]
DEgenesPvalue <- pv[mask]
DEgenesDesc <- mcols(se.filt)[DEgenesEGs, "description"]
DEgenesDesc <- sub(" \\[.+\\]", "", DEgenesDesc)
DEgenesTab <- data.frame(EntrezID=DEgenesEGs,
Symbol=DEgenesSyms,
Description=DEgenesDesc,
"P value"=DEgenesPvalue,
stringsAsFactors=FALSE, check.names=FALSE)
DEgenesTab <- DEgenesTab[order(DEgenesTab[["P value"]]), ] ## order by p-value
rownames(DEgenesTab) <- 1:nrow(DEgenesTab)4.2.1 for volcano
sv <- sva(assays(se.filt.all)$logCPM, mod=mod, mod0=mod0)
Number of significant surrogate variables is: 4
Iteration (out of 5 ):1 2 3 4 5
mod <- cbind(mod, sv$sv)
colnames(mod) <- c(colnames(mod)[1:2], paste0("SV", 1:sv$n))
fit3 <- lmFit(assays(se.filt.all)$logCPM, mod)
fit3 <- eBayes(fit3)
tt3 <- topTable(fit3, coef=2, n=Inf)
DEgenes_no1 <- rownames(tt3)[tt3$adj.P.Val < 0.1]
sort(table(tt3[DEgenes_no1, "chr"]), decreasing=TRUE)
integer(0)
res3 <- decideTests(fit3, p.value=0.1)
genesmd <- data.frame(chr=as.character(seqnames(rowRanges(se.filt.all))), symbol=rowData(se.filt.all)[, 5], stringsAsFactors=FALSE)
fit3$genes <- genesmd
volcanoplot(fit3, coef=2, highlight=7, names=fit3$genes$symbol, main="Known+Unknown covariates", las=1)
mask <- DEgenesTab$EntrezID %in% DEgenes_no3
DEgenesTab <- DEgenesTab[mask,]In the table 3 the DE genes with lowest p-values are displayed:
| EntrezID | Symbol | Description | P value | |
|---|---|---|---|---|
| 2 | 5493 | PPL | periplakin | 4.70e-06 |
| 4 | 117583 | PARD3B | par-3 family cell polarity regulator beta | 1.32e-05 |
| 5 | 79871 | RPAP2 | RNA polymerase II associated protein 2 | 1.39e-05 |
| 7 | 79071 | ELOVL6 | ELOVL fatty acid elongase 6 | 2.26e-05 |
| 8 | 285362 | SUMF1 | sulfatase modifying factor 1 | 2.74e-05 |
| 10 | 5565 | PRKAB2 | protein kinase AMP-activated non-catalytic subunit beta 2 | 3.36e-05 |
| 12 | 6235 | RPS29 | ribosomal protein S29 | 3.87e-05 |
| 13 | 307 | ANXA4 | annexin A4 | 4.12e-05 |
| 14 | 1457 | CSNK2A1 | casein kinase 2 alpha 1 | 4.32e-05 |
| 16 | 282890 | ZNF311 | zinc finger protein 311 | 5.24e-05 |
4.3 Between Colostrum and Mature
Checking the distribution of differentially expressed genes:
se.filt.all <- se.filt[,se.filt$lacStageFac!=2]
se.filt.all$stage <- droplevels(se.filt.all$lacStageFac)
mod <- model.matrix(~ se.filt.all$stage,
colData(se.filt.all))
mod0 <- model.matrix(~ 1, colData(se.filt.all))
pv <- f.pvalue(assays(se.filt.all)$logCPM, mod, mod0)
#sum(p.adjust(pv, method="fdr") < 0.05)
#sum(p.adjust(pv, method="fdr") < 0.1)
hist(pv, main="", las=1)
mask <- p.adjust(pv, method="fdr") < 0.1
DEgenesEGs <- names(pv)[mask]
DEgenesSyms <- mcols(se.filt)[DEgenesEGs, "symbol"]
DEgenesPvalue <- pv[mask]
DEgenesDesc <- mcols(se.filt)[DEgenesEGs, "description"]
DEgenesDesc <- sub(" \\[.+\\]", "", DEgenesDesc)
DEgenesTab <- data.frame(EntrezID=DEgenesEGs,
Symbol=DEgenesSyms,
Description=DEgenesDesc,
"P value"=DEgenesPvalue,
stringsAsFactors=FALSE, check.names=FALSE)
DEgenesTab <- DEgenesTab[order(DEgenesTab[["P value"]]), ] ## order by p-value
rownames(DEgenesTab) <- 1:nrow(DEgenesTab)4.3.1 for volcano
sv <- sva(assays(se.filt.all)$logCPM, mod=mod, mod0=mod0)
Number of significant surrogate variables is: 4
Iteration (out of 5 ):1 2 3 4 5
mod <- cbind(mod, sv$sv)
colnames(mod) <- c(colnames(mod)[1:2], paste0("SV", 1:sv$n))
fit3 <- lmFit(assays(se.filt.all)$logCPM, mod)
fit3 <- eBayes(fit3)
tt3 <- topTable(fit3, coef=2, n=Inf)
DEgenes_no2 <- rownames(tt3)[tt3$adj.P.Val < 0.1]
sort(table(tt3[DEgenes_no2, "chr"]), decreasing=TRUE)
integer(0)
res3 <- decideTests(fit3, p.value=0.1)
genesmd <- data.frame(chr=as.character(seqnames(rowRanges(se.filt.all))), symbol=rowData(se.filt.all)[, 5], stringsAsFactors=FALSE)
fit3$genes <- genesmd
volcanoplot(fit3, coef=2, highlight=7, names=fit3$genes$symbol, main="Known+Unknown covariates", las=1)
mask <- DEgenesTab$EntrezID %in% DEgenes_no2
DEgenesTab <- DEgenesTab[mask,]In the table 4 the DE genes with lowest p-values are displayed:
| EntrezID | Symbol | Description | P value | |
|---|---|---|---|---|
| 1 | 2889 | RAPGEF1 | Rap guanine nucleotide exchange factor 1 | 0 |
| 2 | 116985 | ARAP1 | ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 | 0 |
| 3 | 7094 | TLN1 | talin 1 | 0 |
| 4 | 5230 | PGK1 | phosphoglycerate kinase 1 | 0 |
| 5 | 3073 | HEXA | hexosaminidase subunit alpha | 0 |
| 6 | 5777 | PTPN6 | protein tyrosine phosphatase, non-receptor type 6 | 0 |
| 7 | 3516 | RBPJ | recombination signal binding protein for immunoglobulin kappa J region | 0 |
| 8 | 23313 | KIAA0930 | KIAA0930 | 0 |
| 9 | 23646 | PLD3 | phospholipase D family member 3 | 0 |
| 10 | 5027 | P2RX7 | purinergic receptor P2X 7 | 0 |
The number of DE genes in the three comparisons above are:
- Colostral-Transitional 8028 DE genes
- Transitional-Mature 3299 DE genes
- Colostral-Mature 9151 DE genes.
It is evident that the number of differentially expressed genes that was obtained in each of the three analysis is quite in line with the number that was reported in the paper. There the observed numbers are 8015, 1948 and 8527 respectively. These numbers are quite large and we think it makes sense because of the nature of the tissue, since the milk should adapt to the infant’s needs.
As we mentioned, the sample size is quite small in our case, so that gives rise to different biases which can be dealt with using different strategies, and yielding slightly different results.
5 Functional analysis
Here we will do the functional analysis.
library(org.Hs.eg.db)
library(GOstats)
library(KEGGREST)
geneUniverse <- rownames(se)5.1 Between Colostrum and Transitional (no_3)
5.1.1 Go enrichment
params <- new("GOHyperGParams", geneIds=DEgenesEGs_no3,universeGeneIds=geneUniverse, annotation="org.Hs.eg.db", ontology="BP", pvalueCutoff=0.05, testDirection="over")
conditional(params) <- TRUE
hgOverCond <- hyperGTest(params)
goresults <- summary(hgOverCond)mask <- goresults$OddsRatio != "Inf"
goresults <- goresults[mask, ]
goresults <- goresults[order(goresults$OddsRatio, decreasing=TRUE), ]
goresults
GOBPID Pvalue OddsRatio ExpCount Count Size
109 GO:0019080 4.372384e-06 24.132498 6.786241 16 17
120 GO:0001732 1.066506e-05 22.541471 6.400530 15 16
194 GO:0032486 1.370322e-04 18.025701 5.200430 12 13
195 GO:1903265 1.370322e-04 18.025701 5.200430 12 13
290 GO:0046931 7.289539e-04 15.029038 4.398299 10 11
291 GO:0032790 7.321902e-04 15.017268 4.400364 10 11
292 GO:0033869 7.321902e-04 15.017268 4.400364 10 11
293 GO:0090527 7.321902e-04 15.017268 4.400364 10 11
370 GO:0009113 1.674598e-03 13.513674 4.000331 9 10
371 GO:0060397 1.674598e-03 13.513674 4.000331 9 10
372 GO:0070544 1.674598e-03 13.513674 4.000331 9 10
373 GO:0071233 1.674598e-03 13.513674 4.000331 9 10
374 GO:0090557 1.674598e-03 13.513674 4.000331 9 10
458 GO:0000301 3.796011e-03 12.010496 3.600298 8 9
459 GO:0000467 3.796011e-03 12.010496 3.600298 8 9
460 GO:0006012 3.796011e-03 12.010496 3.600298 8 9
461 GO:0007220 3.796011e-03 12.010496 3.600298 8 9
462 GO:0032287 3.796011e-03 12.010496 3.600298 8 9
463 GO:0072344 3.796011e-03 12.010496 3.600298 8 9
464 GO:0140627 3.796011e-03 12.010496 3.600298 8 9
613 GO:0046825 8.425789e-03 10.535383 3.195226 7 8
614 GO:0006369 8.512085e-03 10.507733 3.200265 7 8
615 GO:0010807 8.512085e-03 10.507733 3.200265 7 8
616 GO:0017038 8.512085e-03 10.507733 3.200265 7 8
617 GO:0043634 8.512085e-03 10.507733 3.200265 7 8
618 GO:0048227 8.512085e-03 10.507733 3.200265 7 8
619 GO:0051683 8.512085e-03 10.507733 3.200265 7 8
620 GO:0090063 8.512085e-03 10.507733 3.200265 7 8
621 GO:0098885 8.512085e-03 10.507733 3.200265 7 8
622 GO:2000586 8.512085e-03 10.507733 3.200265 7 8
623 GO:2000643 8.512085e-03 10.507733 3.200265 7 8
229 GO:0150105 2.760942e-04 9.772476 5.997516 13 15
230 GO:0071243 2.763651e-04 9.771124 5.998013 13 15
232 GO:0019885 2.777230e-04 9.764373 6.000497 13 15
792 GO:0072655 1.846757e-02 9.058988 2.790280 6 7
278 GO:1904925 6.065864e-04 9.012022 5.600464 12 14
804 GO:0006166 1.883163e-02 9.005385 2.800232 6 7
805 GO:0007221 1.883163e-02 9.005385 2.800232 6 7
806 GO:0008635 1.883163e-02 9.005385 2.800232 6 7
807 GO:0019673 1.883163e-02 9.005385 2.800232 6 7
808 GO:0034334 1.883163e-02 9.005385 2.800232 6 7
809 GO:0035666 1.883163e-02 9.005385 2.800232 6 7
810 GO:0045054 1.883163e-02 9.005385 2.800232 6 7
811 GO:0046053 1.883163e-02 9.005385 2.800232 6 7
812 GO:0046719 1.883163e-02 9.005385 2.800232 6 7
813 GO:0061002 1.883163e-02 9.005385 2.800232 6 7
814 GO:0070358 1.883163e-02 9.005385 2.800232 6 7
815 GO:0071029 1.883163e-02 9.005385 2.800232 6 7
816 GO:0071035 1.883163e-02 9.005385 2.800232 6 7
817 GO:0071038 1.883163e-02 9.005385 2.800232 6 7
818 GO:0097052 1.883163e-02 9.005385 2.800232 6 7
819 GO:0106035 1.883163e-02 9.005385 2.800232 6 7
820 GO:0150093 1.883163e-02 9.005385 2.800232 6 7
821 GO:1901098 1.883163e-02 9.005385 2.800232 6 7
822 GO:1902231 1.883163e-02 9.005385 2.800232 6 7
823 GO:2000192 1.883163e-02 9.005385 2.800232 6 7
338 GO:0042059 1.302150e-03 8.270167 5.196554 11 13
339 GO:0035331 1.311761e-03 8.259878 5.200430 11 13
340 GO:1990253 1.311761e-03 8.259878 5.200430 11 13
1147 GO:0034340 4.066451e-02 7.522910 2.396475 5 6
216 GO:0046827 2.136613e-04 7.512441 7.200596 15 18
417 GO:0036444 2.804342e-03 7.507943 4.800397 10 12
418 GO:0051639 2.804342e-03 7.507943 4.800397 10 12
419 GO:0061795 2.804342e-03 7.507943 4.800397 10 12
1152 GO:0015911 4.088882e-02 7.507597 2.399404 5 6
1153 GO:0006552 4.094983e-02 7.503451 2.400199 5 6
1154 GO:0006566 4.094983e-02 7.503451 2.400199 5 6
1155 GO:0019262 4.094983e-02 7.503451 2.400199 5 6
1156 GO:0019346 4.094983e-02 7.503451 2.400199 5 6
1157 GO:0031581 4.094983e-02 7.503451 2.400199 5 6
1158 GO:0032020 4.094983e-02 7.503451 2.400199 5 6
1159 GO:0032799 4.094983e-02 7.503451 2.400199 5 6
1160 GO:0032803 4.094983e-02 7.503451 2.400199 5 6
1161 GO:0034137 4.094983e-02 7.503451 2.400199 5 6
1162 GO:0036115 4.094983e-02 7.503451 2.400199 5 6
1163 GO:0043456 4.094983e-02 7.503451 2.400199 5 6
1164 GO:0044340 4.094983e-02 7.503451 2.400199 5 6
1165 GO:0045046 4.094983e-02 7.503451 2.400199 5 6
1166 GO:0048205 4.094983e-02 7.503451 2.400199 5 6
1167 GO:0051725 4.094983e-02 7.503451 2.400199 5 6
1168 GO:0061087 4.094983e-02 7.503451 2.400199 5 6
1169 GO:0061734 4.094983e-02 7.503451 2.400199 5 6
1170 GO:0070309 4.094983e-02 7.503451 2.400199 5 6
1171 GO:0070427 4.094983e-02 7.503451 2.400199 5 6
1172 GO:0070842 4.094983e-02 7.503451 2.400199 5 6
1173 GO:0086073 4.094983e-02 7.503451 2.400199 5 6
1174 GO:0120183 4.094983e-02 7.503451 2.400199 5 6
1175 GO:1901289 4.094983e-02 7.503451 2.400199 5 6
1176 GO:1901727 4.094983e-02 7.503451 2.400199 5 6
1177 GO:1903301 4.094983e-02 7.503451 2.400199 5 6
1178 GO:1903371 4.094983e-02 7.503451 2.400199 5 6
1179 GO:1903898 4.094983e-02 7.503451 2.400199 5 6
1180 GO:1904352 4.094983e-02 7.503451 2.400199 5 6
1181 GO:1905684 4.094983e-02 7.503451 2.400199 5 6
1182 GO:1990116 4.094983e-02 7.503451 2.400199 5 6
1183 GO:2000323 4.094983e-02 7.503451 2.400199 5 6
1184 GO:2001286 4.094983e-02 7.503451 2.400199 5 6
1185 GO:2001293 4.094983e-02 7.503451 2.400199 5 6
3 GO:0002181 8.499569e-23 7.191080 50.352642 104 126
259 GO:0006744 4.493475e-04 7.010643 6.800563 14 17
260 GO:0046855 4.493475e-04 7.010643 6.800563 14 17
261 GO:1903358 4.493475e-04 7.010643 6.800563 14 17
61 GO:0006413 8.352830e-08 6.911367 15.561949 32 39
544 GO:0015937 5.915433e-03 6.756215 4.400364 9 11
545 GO:0039530 5.915433e-03 6.756215 4.400364 9 11
546 GO:0046504 5.915433e-03 6.756215 4.400364 9 11
547 GO:0051561 5.915433e-03 6.756215 4.400364 9 11
548 GO:0071679 5.915433e-03 6.756215 4.400364 9 11
549 GO:0097384 5.915433e-03 6.756215 4.400364 9 11
202 GO:0007042 1.541591e-04 6.386753 8.400695 17 21
236 GO:0070584 3.151889e-04 6.010231 8.000662 16 20
697 GO:0002084 1.228166e-02 6.004695 4.000331 8 10
698 GO:0010918 1.228166e-02 6.004695 4.000331 8 10
699 GO:0018401 1.228166e-02 6.004695 4.000331 8 10
700 GO:0032261 1.228166e-02 6.004695 4.000331 8 10
701 GO:0033572 1.228166e-02 6.004695 4.000331 8 10
702 GO:0035646 1.228166e-02 6.004695 4.000331 8 10
703 GO:0048194 1.228166e-02 6.004695 4.000331 8 10
704 GO:0048757 1.228166e-02 6.004695 4.000331 8 10
705 GO:0071223 1.228166e-02 6.004695 4.000331 8 10
706 GO:1902237 1.228166e-02 6.004695 4.000331 8 10
707 GO:2000601 1.228166e-02 6.004695 4.000331 8 10
78 GO:0032728 5.549458e-07 5.832364 15.601291 31 39
182 GO:0051438 1.052695e-04 5.722403 9.589917 19 24
283 GO:0097202 6.375333e-04 5.633813 7.600629 15 19
466 GO:0006177 3.897402e-03 5.506079 5.600464 11 14
467 GO:0007175 3.897402e-03 5.506079 5.600464 11 14
468 GO:0035721 3.897402e-03 5.506079 5.600464 11 14
469 GO:0036151 3.897402e-03 5.506079 5.600464 11 14
907 GO:0015986 2.451615e-02 5.283340 3.588037 7 9
908 GO:0022406 2.466192e-02 5.274579 3.591617 7 9
174 GO:0009081 7.284023e-05 5.261621 10.800894 21 27
910 GO:0019068 2.488311e-02 5.261384 3.597016 7 9
913 GO:0006013 2.501834e-02 5.253383 3.600298 7 9
914 GO:0006048 2.501834e-02 5.253383 3.600298 7 9
915 GO:0006072 2.501834e-02 5.253383 3.600298 7 9
916 GO:0006930 2.501834e-02 5.253383 3.600298 7 9
917 GO:0010890 2.501834e-02 5.253383 3.600298 7 9
918 GO:0010994 2.501834e-02 5.253383 3.600298 7 9
919 GO:0015917 2.501834e-02 5.253383 3.600298 7 9
920 GO:0016139 2.501834e-02 5.253383 3.600298 7 9
921 GO:0016559 2.501834e-02 5.253383 3.600298 7 9
922 GO:0045792 2.501834e-02 5.253383 3.600298 7 9
923 GO:0046601 2.501834e-02 5.253383 3.600298 7 9
924 GO:0048845 2.501834e-02 5.253383 3.600298 7 9
925 GO:0051292 2.501834e-02 5.253383 3.600298 7 9
926 GO:0061909 2.501834e-02 5.253383 3.600298 7 9
927 GO:0071225 2.501834e-02 5.253383 3.600298 7 9
928 GO:1900864 2.501834e-02 5.253383 3.600298 7 9
38 GO:0042776 7.387113e-10 5.128341 26.402185 51 66
256 GO:0032402 4.244275e-04 5.108933 8.800728 17 22
257 GO:0044154 4.244275e-04 5.108933 8.800728 17 22
581 GO:0051403 7.542106e-03 5.036039 5.181112 10 13
586 GO:0006901 7.717233e-03 5.012923 5.195402 10 13
587 GO:0006465 7.779613e-03 5.004835 5.200430 10 13
588 GO:0016558 7.779613e-03 5.004835 5.200430 10 13
589 GO:0070424 7.779613e-03 5.004835 5.200430 10 13
590 GO:0070863 7.779613e-03 5.004835 5.200430 10 13
161 GO:1900101 4.874211e-05 4.940394 12.000993 23 30
40 GO:0070936 9.803246e-10 4.902320 27.202252 52 68
298 GO:0022904 7.933740e-04 4.835932 8.371338 16 21
303 GO:0036092 8.304841e-04 4.807742 8.400695 16 21
304 GO:0098780 8.304841e-04 4.807742 8.400695 16 21
178 GO:0042398 9.352125e-05 4.729310 11.594554 22 29
69 GO:0006890 1.612176e-07 4.634805 21.201755 40 53
500 GO:0032481 4.784456e-03 4.521033 6.387075 12 16
752 GO:1903214 1.513752e-02 4.511219 4.795622 9 12
267 GO:0039531 5.361085e-04 4.508090 9.600795 18 24
268 GO:0060907 5.361085e-04 4.508090 9.600795 18 24
269 GO:0061162 5.361085e-04 4.508090 9.600795 18 24
1243 GO:0006825 4.962635e-02 4.507256 3.198145 6 8
1244 GO:0009151 4.963998e-02 4.506842 3.198322 6 8
359 GO:1903232 1.604567e-03 4.506635 8.000662 15 20
509 GO:0044790 4.883282e-03 4.505182 6.400530 12 16
510 GO:0061684 4.883282e-03 4.505182 6.400530 12 16
511 GO:0070131 4.883282e-03 4.505182 6.400530 12 16
512 GO:0071025 4.883282e-03 4.505182 6.400530 12 16
1245 GO:0070071 4.969459e-02 4.505182 3.199028 6 8
753 GO:0019321 1.524870e-02 4.503729 4.800397 9 12
754 GO:0033539 1.524870e-02 4.503729 4.800397 9 12
755 GO:0043476 1.524870e-02 4.503729 4.800397 9 12
756 GO:0090646 1.524870e-02 4.503729 4.800397 9 12
1246 GO:0006616 4.979027e-02 4.502278 3.200265 6 8
1247 GO:0007172 4.979027e-02 4.502278 3.200265 6 8
1248 GO:0010637 4.979027e-02 4.502278 3.200265 6 8
1249 GO:0015846 4.979027e-02 4.502278 3.200265 6 8
1250 GO:0016254 4.979027e-02 4.502278 3.200265 6 8
1251 GO:0031204 4.979027e-02 4.502278 3.200265 6 8
1252 GO:0033615 4.979027e-02 4.502278 3.200265 6 8
1253 GO:0034498 4.979027e-02 4.502278 3.200265 6 8
1254 GO:0035754 4.979027e-02 4.502278 3.200265 6 8
1255 GO:0040016 4.979027e-02 4.502278 3.200265 6 8
1256 GO:0043983 4.979027e-02 4.502278 3.200265 6 8
1257 GO:0045647 4.979027e-02 4.502278 3.200265 6 8
1258 GO:0046784 4.979027e-02 4.502278 3.200265 6 8
1259 GO:0060509 4.979027e-02 4.502278 3.200265 6 8
1260 GO:0060545 4.979027e-02 4.502278 3.200265 6 8
1261 GO:0061511 4.979027e-02 4.502278 3.200265 6 8
1262 GO:0061518 4.979027e-02 4.502278 3.200265 6 8
1263 GO:0070070 4.979027e-02 4.502278 3.200265 6 8
1264 GO:0070127 4.979027e-02 4.502278 3.200265 6 8
1265 GO:0070255 4.979027e-02 4.502278 3.200265 6 8
1266 GO:0071422 4.979027e-02 4.502278 3.200265 6 8
1267 GO:0071499 4.979027e-02 4.502278 3.200265 6 8
1268 GO:0072282 4.979027e-02 4.502278 3.200265 6 8
1269 GO:0072396 4.979027e-02 4.502278 3.200265 6 8
1270 GO:0072423 4.979027e-02 4.502278 3.200265 6 8
1271 GO:0090400 4.979027e-02 4.502278 3.200265 6 8
1272 GO:1902857 4.979027e-02 4.502278 3.200265 6 8
1273 GO:1902966 4.979027e-02 4.502278 3.200265 6 8
1274 GO:1904117 4.979027e-02 4.502278 3.200265 6 8
1275 GO:1904417 4.979027e-02 4.502278 3.200265 6 8
1276 GO:2000973 4.979027e-02 4.502278 3.200265 6 8
432 GO:0036003 3.057055e-03 4.205612 7.600629 14 19
433 GO:0090043 3.057055e-03 4.205612 7.600629 14 19
434 GO:0099563 3.057055e-03 4.205612 7.600629 14 19
631 GO:0009263 9.329646e-03 4.129179 6.000497 11 15
632 GO:0043328 9.329646e-03 4.129179 6.000497 11 15
633 GO:0045176 9.329646e-03 4.129179 6.000497 11 15
634 GO:0046385 9.329646e-03 4.129179 6.000497 11 15
635 GO:0046459 9.329646e-03 4.129179 6.000497 11 15
991 GO:0018394 2.874094e-02 4.021454 4.388102 8 11
995 GO:2000434 2.913472e-02 4.007189 4.397449 8 11
996 GO:0031440 2.916555e-02 4.006083 4.398178 8 11
997 GO:0032495 2.917071e-02 4.005898 4.398299 8 11
998 GO:1903729 2.919131e-02 4.005159 4.398786 8 11
999 GO:0000338 2.925828e-02 4.002762 4.400364 8 11
1000 GO:0006086 2.925828e-02 4.002762 4.400364 8 11
1001 GO:0042276 2.925828e-02 4.002762 4.400364 8 11
1002 GO:0042451 2.925828e-02 4.002762 4.400364 8 11
1003 GO:0042455 2.925828e-02 4.002762 4.400364 8 11
1004 GO:0051340 2.925828e-02 4.002762 4.400364 8 11
1005 GO:0071044 2.925828e-02 4.002762 4.400364 8 11
1006 GO:0071803 2.925828e-02 4.002762 4.400364 8 11
1007 GO:0097400 2.925828e-02 4.002762 4.400364 8 11
1008 GO:1900363 2.925828e-02 4.002762 4.400364 8 11
1009 GO:1902510 2.925828e-02 4.002762 4.400364 8 11
1010 GO:1903059 2.925828e-02 4.002762 4.400364 8 11
1011 GO:2000480 2.925828e-02 4.002762 4.400364 8 11
98 GO:0006120 2.441820e-06 3.978944 20.401689 37 51
250 GO:0043244 3.975970e-04 3.957068 11.580693 21 29
254 GO:0010592 4.090234e-04 3.945490 11.600960 21 29
538 GO:0032648 5.612046e-03 3.918584 7.185267 13 18
540 GO:0006740 5.715276e-03 3.906831 7.198212 13 18
541 GO:0035970 5.734465e-03 3.904671 7.200596 13 18
542 GO:0072663 5.734465e-03 3.904671 7.200596 13 18
543 GO:1905146 5.734465e-03 3.904671 7.200596 13 18
328 GO:0006517 1.198332e-03 3.863722 10.000828 18 25
329 GO:0046835 1.198332e-03 3.863722 10.000828 18 25
88 GO:0070534 1.013238e-06 3.859392 22.801887 41 57
221 GO:0007041 2.483166e-04 3.857032 12.770886 23 32
79 GO:0002753 6.515863e-07 3.810264 24.001987 43 60
289 GO:0090316 7.033021e-04 3.784455 11.152384 20 28
451 GO:0008053 3.524082e-03 3.757609 8.397449 15 21
773 GO:1902176 1.742894e-02 3.755875 5.598145 10 14
453 GO:0090141 3.539773e-03 3.755184 8.400695 15 21
775 GO:0006264 1.748514e-02 3.753281 5.600464 10 14
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85 GO:0009056 9.011208e-07 1.685368 134.801584 179 353
795 GO:1901292 1.859930e-02 1.681980 28.780121 38 72
142 GO:0071496 2.736934e-05 1.678458 101.827626 134 255
472 GO:0060759 3.965681e-03 1.677078 45.521710 60 114
1133 GO:0002931 3.774286e-02 1.675549 22.001821 29 55
320 GO:0070507 1.003165e-03 1.671659 61.605099 81 154
1124 GO:0002711 3.595042e-02 1.669206 22.801887 30 57
1125 GO:0045071 3.595042e-02 1.669206 22.801887 30 57
1126 GO:0070231 3.595042e-02 1.669206 22.801887 30 57
749 GO:0097191 1.508112e-02 1.667112 31.938588 42 80
763 GO:0043154 1.640111e-02 1.665698 31.202583 41 78
764 GO:1901264 1.640111e-02 1.665698 31.202583 41 78
454 GO:0097237 3.641404e-03 1.663432 48.003973 63 120
1075 GO:0035773 3.424483e-02 1.663322 23.601954 31 59
1029 GO:2001243 3.190842e-02 1.662079 24.364913 32 61
155 GO:0034612 4.209891e-05 1.661824 100.808344 132 252
747 GO:2001057 1.494795e-02 1.657518 32.802715 43 82
972 GO:0032984 2.625882e-02 1.656158 26.679797 35 67
438 GO:0033875 3.188236e-03 1.655743 50.404172 66 126
439 GO:0034032 3.188236e-03 1.655743 50.404172 66 126
725 GO:0072331 1.313921e-02 1.655237 34.339913 45 86
742 GO:0000281 1.427041e-02 1.653740 33.602781 44 84
225 GO:0000302 2.661265e-04 1.648431 81.206721 106 203
68 GO:0045893 1.601136e-07 1.644965 175.933456 229 444
987 GO:1901224 2.821084e-02 1.643506 26.802218 35 67
519 GO:0007266 5.020551e-03 1.640913 46.772848 61 117
688 GO:1900542 1.185470e-02 1.640378 36.803046 48 92
978 GO:0061077 2.688073e-02 1.639313 27.602285 36 69
678 GO:1900407 1.131796e-02 1.637417 37.603112 49 94
642 GO:0051494 1.002689e-02 1.635461 39.152240 51 98
905 GO:0006493 2.417567e-02 1.633246 29.185484 38 73
717 GO:0010557 1.292267e-02 1.629801 35.993625 47 92
473 GO:0051225 4.074320e-03 1.628449 50.804205 66 127
900 GO:0006809 2.326436e-02 1.628155 30.002483 39 75
355 GO:1902115 1.427157e-03 1.627605 63.916796 83 160
974 GO:0007005 2.644778e-02 1.624532 28.418262 37 72
95 GO:0042326 2.001532e-06 1.622679 152.412615 197 381
772 GO:0032271 1.726586e-02 1.621710 33.897096 44 85
837 GO:0000380 2.014676e-02 1.618747 32.402682 42 81
326 GO:0046578 1.119081e-03 1.617511 68.761989 89 172
1234 GO:0043966 4.828704e-02 1.616405 22.376485 29 56
829 GO:0061515 1.920589e-02 1.615931 33.202748 43 83
1237 GO:0030330 4.858070e-02 1.615134 22.387008 29 56
1239 GO:0072348 4.899755e-02 1.613343 22.401854 29 56
791 GO:0032092 1.831017e-02 1.613256 34.002814 44 85
306 GO:0044242 8.478313e-04 1.611225 73.543021 95 184
774 GO:0019915 1.745734e-02 1.610712 34.802881 45 87
176 GO:0051726 7.940603e-05 1.610328 105.327403 136 265
679 GO:1901576 1.141442e-02 1.610200 36.375904 48 102
1222 GO:0048008 4.656628e-02 1.609443 23.201920 30 58
1223 GO:0051058 4.656628e-02 1.609443 23.201920 30 58
198 GO:0006796 1.436424e-04 1.608759 94.664849 123 247
1201 GO:0043407 4.426389e-02 1.605818 24.001987 31 60
164 GO:0010638 4.968271e-05 1.605014 113.264331 146 285
520 GO:0046488 5.046023e-03 1.604352 51.160374 66 128
99 GO:0033554 2.456622e-06 1.603958 153.258664 198 395
751 GO:1903312 1.513560e-02 1.603777 37.203079 48 93
1143 GO:0000045 3.923012e-02 1.602994 25.566718 33 64
1189 GO:0032387 4.208287e-02 1.602439 24.802053 32 62
353 GO:0022613 1.400416e-03 1.601075 68.222709 88 172
493 GO:1900180 4.500154e-03 1.597778 53.604437 69 134
341 GO:0061025 1.317708e-03 1.594453 70.805861 91 177
180 GO:0043543 9.883481e-05 1.590653 108.408973 139 271
990 GO:0046434 2.868985e-02 1.589470 30.340171 39 76
408 GO:0043603 2.490890e-03 1.586334 62.120150 80 159
636 GO:0007229 9.441499e-03 1.586291 45.203742 58 113
398 GO:0031330 2.157551e-03 1.585468 65.509091 84 164
591 GO:0008286 7.828608e-03 1.581023 48.404006 62 121
351 GO:0032535 1.380670e-03 1.580873 72.635634 93 182
1241 GO:0016071 4.907152e-02 1.579393 24.149550 31 61
385 GO:0071453 1.889049e-03 1.578231 68.805695 88 172
895 GO:0031398 2.274455e-02 1.577699 34.363868 44 86
906 GO:0032418 2.438214e-02 1.576373 33.602781 43 84
129 GO:0019637 1.697071e-05 1.575147 138.520864 177 351
255 GO:0045862 4.090974e-04 1.571577 92.459374 118 232
494 GO:0031344 4.556961e-03 1.570297 57.109370 73 144
836 GO:0045185 2.006789e-02 1.570147 36.803046 47 92
172 GO:0044770 6.899560e-05 1.570040 120.069472 153 301
626 GO:0034976 8.869826e-03 1.565057 48.608686 62 122
46 GO:0036211 3.349286e-09 1.564739 275.651158 351 724
437 GO:0007015 3.166129e-03 1.563831 63.519121 81 160
680 GO:0043393 1.146219e-02 1.561469 45.540585 58 114
683 GO:0043488 1.149984e-02 1.561095 45.546980 58 114
1214 GO:0009059 4.571879e-02 1.560989 24.783683 32 67
238 GO:0033044 3.235694e-04 1.558349 100.008278 127 250
378 GO:0018393 1.786968e-03 1.556452 74.006125 94 185
596 GO:0019827 7.900698e-03 1.554296 51.952528 66 130
597 GO:0044272 7.992488e-03 1.553129 51.975588 66 130
220 GO:0033365 2.308635e-04 1.553034 105.418240 134 268
559 GO:0055076 6.412128e-03 1.548639 56.004636 71 140
1128 GO:0046822 3.614912e-02 1.547619 30.737852 39 77
1148 GO:0019079 4.073494e-02 1.546818 29.173328 37 73
1142 GO:2001021 3.906255e-02 1.544246 29.990064 38 75
1132 GO:0034121 3.737984e-02 1.542178 30.802550 39 77
424 GO:0010950 2.911414e-03 1.541242 69.605761 88 174
411 GO:0031503 2.654960e-03 1.540591 71.205894 90 178
310 GO:0070085 8.582881e-04 1.536860 90.342576 114 226
111 GO:0010563 5.557059e-06 1.536777 176.414602 222 441
147 GO:1901135 3.144116e-05 1.536312 145.039515 183 367
798 GO:0006664 1.873093e-02 1.532529 42.003477 53 105
799 GO:1901655 1.873093e-02 1.532529 42.003477 53 105
786 GO:0050779 1.784496e-02 1.532054 42.803543 54 107
100 GO:0016567 2.635890e-06 1.522176 197.052516 247 497
112 GO:0006468 5.964003e-06 1.513561 187.127899 234 473
1129 GO:0006643 3.685966e-02 1.507279 34.341705 43 86
1137 GO:0006906 3.895519e-02 1.506544 33.551697 42 84
429 GO:0031345 3.028006e-03 1.506501 76.806357 96 192
565 GO:0044087 6.694798e-03 1.505768 62.242701 78 158
1121 GO:0031123 3.545748e-02 1.505565 35.164991 44 88
929 GO:0031058 2.551971e-02 1.503334 40.803377 51 102
977 GO:0036473 2.680684e-02 1.503264 40.003311 50 100
1127 GO:0001510 3.611734e-02 1.502845 35.202914 44 88
136 GO:0061024 2.140934e-05 1.499929 171.054491 213 431
264 GO:0010975 4.784411e-04 1.492914 115.023657 143 288
117 GO:0019538 9.540761e-06 1.491871 182.861473 229 496
37 GO:0031325 5.754904e-10 1.491543 396.068071 489 1014
508 GO:0032200 4.867804e-03 1.489388 72.405993 90 181
628 GO:0010675 8.947217e-03 1.485724 62.005132 77 155
710 GO:0000086 1.246433e-02 1.483337 56.404669 70 141
720 GO:0042157 1.307228e-02 1.482965 55.604602 69 139
740 GO:0006997 1.371085e-02 1.482584 54.804536 68 137
175 GO:0001701 7.531977e-05 1.482404 156.812979 194 392
30 GO:0006996 5.248659e-11 1.480378 460.571429 567 1209
865 GO:0042752 2.113723e-02 1.478693 47.603940 59 119
893 GO:0071887 2.218866e-02 1.478199 46.803874 58 117
1096 GO:0030258 3.482410e-02 1.477964 38.714889 48 97
901 GO:0098586 2.329476e-02 1.477691 46.003808 57 115
140 GO:1901575 2.474609e-05 1.475778 179.106985 222 464
988 GO:0061014 2.832967e-02 1.475496 42.803543 53 107
5 GO:0071840 5.073541e-22 1.474290 1223.196511 1459 3228
265 GO:0044089 5.088535e-04 1.473428 121.404629 150 305
1082 GO:2001237 3.452022e-02 1.472994 39.603278 49 99
1135 GO:0045807 3.813738e-02 1.471605 38.003146 47 95
266 GO:0044403 5.237185e-04 1.470898 122.410132 151 306
1146 GO:0030516 4.009485e-02 1.470871 37.203079 46 93
81 GO:0007049 7.006165e-07 1.470325 265.090042 326 670
465 GO:0030522 3.877758e-03 1.469718 81.784330 101 205
77 GO:1901566 4.823417e-07 1.469658 270.221093 333 695
1208 GO:0034644 4.433805e-02 1.469313 35.602947 44 89
1238 GO:0006497 4.867996e-02 1.468847 33.985919 42 85
1240 GO:0051453 4.906470e-02 1.467624 34.002814 42 85
796 GO:0030163 1.863189e-02 1.467502 50.860059 63 130
153 GO:0008219 3.972797e-05 1.467133 177.735749 219 451
695 GO:0032872 1.222589e-02 1.467130 59.955189 74 150
721 GO:0071456 1.310356e-02 1.464476 59.204900 73 148
781 GO:0006486 1.753286e-02 1.464318 53.507848 66 134
575 GO:0006397 7.315362e-03 1.464279 70.549388 87 177
750 GO:1903900 1.511274e-02 1.462599 56.804702 70 142
827 GO:0035303 1.919672e-02 1.459140 52.804371 65 132
369 GO:0051607 1.648099e-03 1.455756 104.223863 128 261
986 GO:0000077 2.803449e-02 1.453521 46.384632 57 116
499 GO:0051223 4.777598e-03 1.452725 82.212519 101 207
24 GO:0010556 6.093549e-13 1.452631 646.824654 782 1659
1012 GO:0030004 2.968836e-02 1.451564 45.603775 56 114
32 GO:0018193 2.486814e-10 1.449613 491.496320 596 1230
1188 GO:0097306 4.193110e-02 1.443979 40.003311 49 100
302 GO:0120031 8.236766e-04 1.441735 125.175365 153 315
1220 GO:0046330 4.633524e-02 1.441439 38.403179 47 96
1221 GO:0061097 4.633524e-02 1.441439 38.403179 47 96
239 GO:0006915 3.237254e-04 1.437900 148.262192 181 376
388 GO:1901564 2.021580e-03 1.432644 100.377280 124 282
1016 GO:2000278 3.089553e-02 1.430728 48.404006 59 121
227 GO:0046486 2.690155e-04 1.430380 158.813145 193 397
243 GO:0044782 3.360887e-04 1.427990 154.812814 188 387
222 GO:0019752 2.510717e-04 1.427871 161.302204 196 406
640 GO:0030036 9.927910e-03 1.425774 73.891903 90 187
274 GO:1901653 5.584892e-04 1.422953 145.143883 176 363
10 GO:1903506 6.189120e-20 1.418717 1354.112080 1589 3385
572 GO:1903311 7.136640e-03 1.414713 85.878356 104 215
211 GO:0051301 2.041316e-04 1.413414 177.188912 214 444
151 GO:2000112 3.863839e-05 1.412481 223.107565 269 558
12 GO:0051252 4.684093e-19 1.411905 1318.426664 1545 3317
594 GO:0022411 7.837123e-03 1.411794 84.256106 102 212
984 GO:0051222 2.774227e-02 1.410973 54.499555 66 137
60 GO:0032774 7.867397e-08 1.409106 400.460870 481 1032
107 GO:0006357 4.255926e-06 1.409070 285.673147 344 728
11 GO:0031326 3.741539e-19 1.408402 1360.474031 1590 3429
1015 GO:2001233 3.065513e-02 1.407687 52.909899 64 133
71 GO:0000122 2.138244e-07 1.406930 379.631422 455 949
200 GO:0044283 1.460218e-04 1.405105 192.733903 232 483
1210 GO:0043200 4.460181e-02 1.401935 45.588674 55 114
828 GO:0030307 1.920420e-02 1.399566 66.405496 80 166
280 GO:0051656 6.237797e-04 1.397661 158.145985 190 396
864 GO:1902850 2.108361e-02 1.396936 64.805364 78 162
970 GO:0006518 2.619331e-02 1.395375 58.869525 71 150
745 GO:0000910 1.493899e-02 1.395286 74.006125 89 185
746 GO:2000045 1.493899e-02 1.395286 74.006125 89 185
74 GO:0006351 3.525311e-07 1.394153 380.557243 455 982
381 GO:0000375 1.839003e-03 1.393628 130.810827 157 327
16 GO:0080090 1.016468e-16 1.392782 1246.095890 1450 3220
554 GO:0006260 6.235293e-03 1.391568 98.299320 118 246
242 GO:0006325 3.340499e-04 1.389556 182.100434 218 456
282 GO:1901137 6.300241e-04 1.387454 164.515891 197 414
26 GO:0045935 3.215405e-12 1.387338 811.667182 956 2029
641 GO:0071902 9.949304e-03 1.386994 87.607251 105 219
674 GO:0022008 1.060769e-02 1.386034 85.918071 103 216
1198 GO:0022612 4.387249e-02 1.385761 49.204073 59 123
253 GO:0051090 4.081930e-04 1.384138 180.814966 216 452
65 GO:0044260 1.207553e-07 1.380431 436.965165 520 1145
909 GO:0051100 2.485258e-02 1.380374 65.205397 78 163
29 GO:0051171 4.860072e-11 1.379889 738.846872 869 1936
131 GO:0006082 1.754940e-05 1.379372 283.166937 337 711
210 GO:0007346 2.027703e-04 1.379352 206.417085 246 516
691 GO:0006520 1.210662e-02 1.378264 85.343897 102 214
981 GO:0040029 2.727580e-02 1.377260 63.605265 76 159
205 GO:0034248 1.651104e-04 1.376163 215.940381 257 540
294 GO:0002764 7.489124e-04 1.375130 169.614039 202 424
426 GO:0046394 2.984081e-03 1.373772 128.410629 153 321
896 GO:0008361 2.286515e-02 1.373292 69.573101 83 174
1192 GO:0070304 4.275127e-02 1.372615 52.804371 63 132
56 GO:1902679 3.124221e-08 1.371309 518.842945 612 1297
1211 GO:0034968 4.483615e-02 1.370628 52.004304 62 130
165 GO:0010941 5.274909e-05 1.370467 258.655059 307 651
782 GO:0010639 1.757403e-02 1.367085 78.972883 94 198
47 GO:0045934 3.567758e-09 1.366818 614.450858 722 1536
193 GO:0043085 1.324893e-04 1.365498 233.630838 277 588
638 GO:0090305 9.681926e-03 1.365029 97.608079 116 244
1022 GO:0043547 3.147916e-02 1.365021 63.038498 75 158
4 GO:0006725 2.114779e-22 1.360873 2477.405055 2781 6193
576 GO:1901988 7.357232e-03 1.359355 108.809006 129 272
428 GO:1901565 3.013052e-03 1.359263 134.676448 160 345
1194 GO:0048813 4.355118e-02 1.359248 55.604602 66 139
1054 GO:0044409 3.347874e-02 1.358948 63.205231 75 158
42 GO:1902680 1.910801e-09 1.357358 672.055626 786 1680
744 GO:0071214 1.488435e-02 1.357310 87.714095 104 220
1105 GO:0010976 3.506517e-02 1.357117 62.405165 74 156
741 GO:0031323 1.396389e-02 1.356269 85.381818 102 231
564 GO:0006281 6.616396e-03 1.353335 114.916111 136 289
794 GO:0045216 1.858492e-02 1.353213 82.806854 98 207
6 GO:1901360 5.661842e-22 1.353073 2573.012968 2876 6432
758 GO:0010810 1.578309e-02 1.351053 88.807351 105 222
209 GO:0032870 1.990053e-04 1.350951 237.619668 280 594
400 GO:0045859 2.184671e-03 1.350945 153.231899 181 385
217 GO:0051338 2.171455e-04 1.348738 235.946110 278 594
1200 GO:0035264 4.422413e-02 1.347276 58.404834 69 146
563 GO:0002831 6.583215e-03 1.343289 121.371188 143 304
1236 GO:0033135 4.853957e-02 1.342985 56.804702 67 142
894 GO:0006479 2.252301e-02 1.339217 82.406821 97 206
271 GO:0043068 5.433842e-04 1.335815 218.418078 256 546
327 GO:0033674 1.130788e-03 1.334529 191.947005 225 480
45 GO:0044238 3.136970e-09 1.333753 794.610290 912 2309
456 GO:0018108 3.681472e-03 1.329696 152.012582 178 380
1023 GO:0016570 3.150061e-02 1.326579 75.924668 89 191
17 GO:0051234 4.545012e-15 1.326540 1600.188163 1813 4038
803 GO:0000398 1.883023e-02 1.321733 96.679268 113 242
801 GO:0051259 1.880805e-02 1.320239 97.608079 114 244
1019 GO:0034470 3.121879e-02 1.312374 82.385931 96 207
834 GO:0016192 1.989959e-02 1.311466 98.596329 115 252
14 GO:0048518 2.440646e-17 1.307345 2472.862321 2736 6194
177 GO:0050790 8.357178e-05 1.303551 346.942109 401 885
1232 GO:0048771 4.816378e-02 1.300133 71.605927 83 179
1048 GO:0002573 3.289986e-02 1.298857 87.207218 101 218
1049 GO:0043491 3.289986e-02 1.298857 87.207218 101 218
156 GO:0051128 4.418398e-05 1.298095 389.509871 449 998
322 GO:0070925 1.049811e-03 1.291630 248.309294 286 625
276 GO:1901699 5.887738e-04 1.288957 282.823409 325 707
771 GO:0010720 1.709851e-02 1.287228 122.410132 141 306
1219 GO:1903828 4.632969e-02 1.283274 80.806688 93 202
669 GO:0032259 1.052071e-02 1.276921 154.412781 177 386
93 GO:0009890 1.310946e-06 1.275801 676.856023 768 1692
762 GO:0062012 1.639171e-02 1.274896 134.411125 154 336
1050 GO:0051402 3.299536e-02 1.274287 101.208377 116 253
759 GO:0045892 1.581440e-02 1.273807 136.101561 156 344
335 GO:0009792 1.272462e-03 1.273752 269.622317 308 674
709 GO:0006631 1.241925e-02 1.269822 153.106926 175 383
23 GO:0090304 5.908704e-13 1.269505 2064.847290 2277 5175
689 GO:0044093 1.186865e-02 1.269260 154.750841 177 392
245 GO:0120036 3.524268e-04 1.266255 357.710830 407 904
488 GO:0060627 4.293001e-03 1.264781 216.817946 247 542
577 GO:0042981 7.405023e-03 1.263822 186.846163 213 471
629 GO:0042060 9.189024e-03 1.263380 176.414602 201 441
967 GO:0051345 2.570133e-02 1.262479 121.882083 139 306
975 GO:0036293 2.650680e-02 1.260853 122.010099 139 305
183 GO:0051246 1.054780e-04 1.260791 447.137425 507 1144
1145 GO:0001558 3.964285e-02 1.259785 101.815372 116 255
286 GO:1902531 6.606841e-04 1.258317 337.433997 383 859
899 GO:0030111 2.325307e-02 1.256553 132.810993 151 332
1233 GO:1902532 4.826796e-02 1.251456 96.835616 110 244
219 GO:0048666 2.273707e-04 1.247986 442.836654 499 1107
550 GO:0010035 6.086803e-03 1.247787 222.818443 252 557
568 GO:1903047 6.919232e-03 1.244502 219.512831 248 551
102 GO:0048583 3.197571e-06 1.239364 833.554664 929 2109
173 GO:0010648 6.920736e-05 1.239210 567.646984 636 1419
1217 GO:0071559 4.592729e-02 1.237477 110.809172 125 277
529 GO:0048858 5.174448e-03 1.234567 258.021356 290 645
184 GO:0051641 1.062864e-04 1.232051 552.699409 619 1455
994 GO:0071692 2.896558e-02 1.230321 146.812152 165 367
309 GO:0002520 8.577156e-04 1.229168 407.633740 456 1019
189 GO:0023057 1.213661e-04 1.229055 570.047183 636 1425
97 GO:0048523 2.331748e-06 1.228453 960.530414 1063 2439
793 GO:0009314 1.855772e-02 1.227958 180.014900 202 450
121 GO:0023051 1.100188e-05 1.227138 804.444358 893 2031
1226 GO:0060070 4.737012e-02 1.224627 120.366768 135 301
976 GO:0045786 2.668495e-02 1.222886 161.613377 181 404
1081 GO:0006066 3.451360e-02 1.221225 145.612052 163 364
363 GO:0051174 1.628039e-03 1.220054 384.736199 429 968
389 GO:0040007 2.055773e-03 1.219919 366.830363 409 917
134 GO:0010646 1.989956e-05 1.219641 801.383786 887 2024
729 GO:0022607 1.322786e-02 1.219457 213.390914 239 555
1193 GO:0009100 4.346806e-02 1.219428 131.377727 147 329
1242 GO:0000226 4.943521e-02 1.218282 123.351880 138 310
354 GO:0060548 1.418872e-03 1.215607 413.634237 460 1034
890 GO:0006897 2.168634e-02 1.213862 190.114590 212 476
930 GO:0008610 2.554507e-02 1.212826 178.447427 199 449
524 GO:0065003 5.121761e-03 1.212438 308.018443 343 785
1225 GO:0051604 4.718813e-02 1.212305 133.611059 149 334
415 GO:0010243 2.693177e-03 1.211181 371.820808 413 931
748 GO:0000904 1.505293e-02 1.209817 226.491818 252 568
431 GO:0030097 3.040849e-03 1.209265 367.630429 408 919
1024 GO:0043434 3.172514e-02 1.209090 168.013907 187 420
1235 GO:0048545 4.838637e-02 1.208974 135.611225 151 339
332 GO:0045944 1.216537e-03 1.207134 461.451986 511 1156
498 GO:0042325 4.750102e-03 1.206532 334.403930 371 842
1230 GO:0009306 4.809081e-02 1.205419 140.330242 156 351
624 GO:0010564 8.537622e-03 1.203012 292.424204 324 731
496 GO:0045937 4.601032e-03 1.200063 360.029800 398 900
599 GO:0032989 8.033635e-03 1.200058 306.425363 339 766
983 GO:0009991 2.750473e-02 1.196265 201.616688 223 504
1025 GO:0061564 3.185070e-02 1.192382 195.616191 216 489
1144 GO:0048812 3.937610e-02 1.182722 193.735680 213 485
1218 GO:0045785 4.594454e-02 1.175939 191.615860 210 479
343 GO:0042592 1.337900e-03 1.169446 677.656090 736 1694
1134 GO:0071407 3.809682e-02 1.168351 229.942871 251 575
708 GO:0051172 1.234321e-02 1.168261 368.754839 402 937
1212 GO:0030335 4.503632e-02 1.162081 226.018708 246 565
525 GO:0009967 5.133116e-03 1.159162 546.613477 592 1373
1072 GO:0001934 3.396615e-02 1.152143 295.624469 320 739
555 GO:0048585 6.270357e-03 1.144395 628.995111 676 1577
423 GO:0032879 2.887041e-03 1.139492 846.870095 906 2117
1224 GO:0071345 4.696322e-02 1.137436 302.355298 325 757
1199 GO:0043066 4.411371e-02 1.135020 324.196383 348 812
824 GO:0048699 1.883655e-02 1.124130 579.247944 617 1448
1186 GO:0007167 4.144985e-02 1.123063 403.233376 430 1008
761 GO:0050793 1.607510e-02 1.099106 1005.574030 1055 2517
904 GO:0010468 2.409469e-02 1.070752 1936.990565 1995 4879
Term
109 viral gene expression
120 formation of cytoplasmic translation initiation complex
194 Rap protein signal transduction
195 positive regulation of tumor necrosis factor-mediated signaling pathway
290 pore complex assembly
291 ribosome disassembly
292 nucleoside bisphosphate catabolic process
293 actin filament reorganization
370 purine nucleobase biosynthetic process
371 growth hormone receptor signaling pathway via JAK-STAT
372 histone H3-K36 demethylation
373 cellular response to leucine
374 establishment of endothelial intestinal barrier
458 retrograde transport, vesicle recycling within Golgi
459 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
460 galactose metabolic process
461 Notch receptor processing
462 peripheral nervous system myelin maintenance
463 rescue of stalled ribosome
464 ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
613 regulation of protein export from nucleus
614 termination of RNA polymerase II transcription
615 regulation of synaptic vesicle priming
616 protein import
617 polyadenylation-dependent ncRNA catabolic process
618 plasma membrane to endosome transport
619 establishment of Golgi localization
620 positive regulation of microtubule nucleation
621 modification of postsynaptic actin cytoskeleton
622 regulation of platelet-derived growth factor receptor-beta signaling pathway
623 positive regulation of early endosome to late endosome transport
229 protein localization to cell-cell junction
230 cellular response to arsenic-containing substance
232 antigen processing and presentation of endogenous peptide antigen via MHC class I
792 establishment of protein localization to mitochondrion
278 positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization
804 purine ribonucleoside salvage
805 positive regulation of transcription of Notch receptor target
806 activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c
807 GDP-mannose metabolic process
808 adherens junction maintenance
809 TRIF-dependent toll-like receptor signaling pathway
810 constitutive secretory pathway
811 dAMP metabolic process
812 regulation by virus of viral protein levels in host cell
813 negative regulation of dendritic spine morphogenesis
814 actin polymerization-dependent cell motility
815 nuclear ncRNA surveillance
816 nuclear polyadenylation-dependent rRNA catabolic process
817 nuclear polyadenylation-dependent tRNA catabolic process
818 L-kynurenine metabolic process
819 protein maturation by [4Fe-4S] cluster transfer
820 amyloid-beta clearance by transcytosis
821 positive regulation of autophagosome maturation
822 positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage
823 negative regulation of fatty acid transport
338 negative regulation of epidermal growth factor receptor signaling pathway
339 negative regulation of hippo signaling
340 cellular response to leucine starvation
1147 response to type I interferon
216 positive regulation of protein export from nucleus
417 calcium import into the mitochondrion
418 actin filament network formation
419 Golgi lumen acidification
1152 long-chain fatty acid import across plasma membrane
1153 leucine catabolic process
1154 threonine metabolic process
1155 N-acetylneuraminate catabolic process
1156 transsulfuration
1157 hemidesmosome assembly
1158 ISG15-protein conjugation
1159 low-density lipoprotein receptor particle metabolic process
1160 regulation of low-density lipoprotein particle receptor catabolic process
1161 positive regulation of toll-like receptor 2 signaling pathway
1162 fatty-acyl-CoA catabolic process
1163 regulation of pentose-phosphate shunt
1164 canonical Wnt signaling pathway involved in regulation of cell proliferation
1165 protein import into peroxisome membrane
1166 COPI coating of Golgi vesicle
1167 protein de-ADP-ribosylation
1168 positive regulation of histone H3-K27 methylation
1169 parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization
1170 lens fiber cell morphogenesis
1171 nucleotide-binding oligomerization domain containing 1 signaling pathway
1172 aggresome assembly
1173 bundle of His cell-Purkinje myocyte adhesion involved in cell communication
1174 positive regulation of focal adhesion disassembly
1175 succinyl-CoA catabolic process
1176 positive regulation of histone deacetylase activity
1177 positive regulation of hexokinase activity
1178 regulation of endoplasmic reticulum tubular network organization
1179 negative regulation of PERK-mediated unfolded protein response
1180 positive regulation of protein catabolic process in the vacuole
1181 regulation of plasma membrane repair
1182 ribosome-associated ubiquitin-dependent protein catabolic process
1183 negative regulation of glucocorticoid receptor signaling pathway
1184 regulation of caveolin-mediated endocytosis
1185 malonyl-CoA metabolic process
3 cytoplasmic translation
259 ubiquinone biosynthetic process
260 inositol phosphate dephosphorylation
261 regulation of Golgi organization
61 translational initiation
544 coenzyme A biosynthetic process
545 MDA-5 signaling pathway
546 glycerol ether biosynthetic process
547 positive regulation of mitochondrial calcium ion concentration
548 commissural neuron axon guidance
549 cellular lipid biosynthetic process
202 lysosomal lumen acidification
236 mitochondrion morphogenesis
697 protein depalmitoylation
698 positive regulation of mitochondrial membrane potential
699 peptidyl-proline hydroxylation to 4-hydroxy-L-proline
700 purine nucleotide salvage
701 transferrin transport
702 endosome to melanosome transport
703 Golgi vesicle budding
704 pigment granule maturation
705 cellular response to lipoteichoic acid
706 positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
707 positive regulation of Arp2/3 complex-mediated actin nucleation
78 positive regulation of interferon-beta production
182 regulation of ubiquitin-protein transferase activity
283 activation of cysteine-type endopeptidase activity
466 GMP biosynthetic process
467 negative regulation of epidermal growth factor-activated receptor activity
468 intraciliary retrograde transport
469 phosphatidylcholine acyl-chain remodeling
907 proton motive force-driven ATP synthesis
908 membrane docking
174 branched-chain amino acid metabolic process
910 virion assembly
913 mannose metabolic process
914 UDP-N-acetylglucosamine biosynthetic process
915 glycerol-3-phosphate metabolic process
916 substrate-dependent cell migration, cell extension
917 positive regulation of sequestering of triglyceride
918 free ubiquitin chain polymerization
919 aminophospholipid transport
920 glycoside catabolic process
921 peroxisome fission
922 negative regulation of cell size
923 positive regulation of centriole replication
924 venous blood vessel morphogenesis
925 nuclear pore complex assembly
926 autophagosome-lysosome fusion
927 cellular response to muramyl dipeptide
928 mitochondrial RNA modification
38 proton motive force-driven mitochondrial ATP synthesis
256 melanosome transport
257 histone H3-K14 acetylation
581 stress-activated MAPK cascade
586 vesicle coating
587 signal peptide processing
588 protein import into peroxisome matrix
589 regulation of nucleotide-binding oligomerization domain containing signaling pathway
590 positive regulation of protein exit from endoplasmic reticulum
161 regulation of endoplasmic reticulum unfolded protein response
40 protein K48-linked ubiquitination
298 respiratory electron transport chain
303 phosphatidylinositol-3-phosphate biosynthetic process
304 response to mitochondrial depolarisation
178 cellular modified amino acid biosynthetic process
69 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
500 positive regulation of type I interferon production
752 regulation of protein targeting to mitochondrion
267 regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
268 positive regulation of macrophage cytokine production
269 establishment of monopolar cell polarity
1243 copper ion transport
1244 purine deoxyribonucleotide metabolic process
359 melanosome assembly
509 suppression of viral release by host
510 chaperone-mediated autophagy
511 positive regulation of mitochondrial translation
512 RNA surveillance
1245 proton-transporting two-sector ATPase complex assembly
753 pentose metabolic process
754 fatty acid beta-oxidation using acyl-CoA dehydrogenase
755 pigment accumulation
756 mitochondrial tRNA processing
1246 SRP-dependent cotranslational protein targeting to membrane, translocation
1247 signal complex assembly
1248 negative regulation of mitochondrial fusion
1249 polyamine transport
1250 preassembly of GPI anchor in ER membrane
1251 post-translational protein targeting to membrane, translocation
1252 mitochondrial proton-transporting ATP synthase complex assembly
1253 early endosome to Golgi transport
1254 B cell chemotaxis
1255 embryonic cleavage
1256 histone H4-K12 acetylation
1257 negative regulation of erythrocyte differentiation
1258 viral mRNA export from host cell nucleus
1259 type I pneumocyte differentiation
1260 positive regulation of necroptotic process
1261 centriole elongation
1262 microglial cell proliferation
1263 proton-transporting V-type ATPase complex assembly
1264 tRNA aminoacylation for mitochondrial protein translation
1265 regulation of mucus secretion
1266 succinate transmembrane transport
1267 cellular response to laminar fluid shear stress
1268 metanephric nephron tubule morphogenesis
1269 response to cell cycle checkpoint signaling
1270 response to DNA damage checkpoint signaling
1271 stress-induced premature senescence
1272 positive regulation of non-motile cilium assembly
1273 positive regulation of protein localization to early endosome
1274 cellular response to vasopressin
1275 positive regulation of xenophagy
1276 regulation of pro-B cell differentiation
432 positive regulation of transcription from RNA polymerase II promoter in response to stress
433 regulation of tubulin deacetylation
434 modification of synaptic structure
631 deoxyribonucleotide biosynthetic process
632 protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
633 apical protein localization
634 deoxyribose phosphate biosynthetic process
635 short-chain fatty acid metabolic process
991 peptidyl-lysine acetylation
995 regulation of protein neddylation
996 regulation of mRNA 3'-end processing
997 response to muramyl dipeptide
998 regulation of plasma membrane organization
999 protein deneddylation
1000 acetyl-CoA biosynthetic process from pyruvate
1001 error-prone translesion synthesis
1002 purine nucleoside biosynthetic process
1003 ribonucleoside biosynthetic process
1004 regulation of ligase activity
1005 histone mRNA catabolic process
1006 positive regulation of podosome assembly
1007 interleukin-17-mediated signaling pathway
1008 regulation of mRNA polyadenylation
1009 regulation of apoptotic DNA fragmentation
1010 regulation of protein lipidation
1011 negative regulation of cAMP-dependent protein kinase activity
98 mitochondrial electron transport, NADH to ubiquinone
250 regulation of protein-containing complex disassembly
254 positive regulation of lamellipodium assembly
538 regulation of interferon-beta production
540 NADPH regeneration
541 peptidyl-threonine dephosphorylation
542 establishment of protein localization to peroxisome
543 lysosomal protein catabolic process
328 protein deglycosylation
329 carbohydrate phosphorylation
88 protein K63-linked ubiquitination
221 lysosomal transport
79 cytoplasmic pattern recognition receptor signaling pathway
289 positive regulation of intracellular protein transport
451 mitochondrial fusion
773 negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
453 positive regulation of mitochondrial fission
775 mitochondrial DNA replication
776 cerebellar Purkinje cell layer formation
777 histone H3-K9 demethylation
778 positive regulation of MHC class II biosynthetic process
779 positive regulation of viral entry into host cell
780 semaphorin-plexin signaling pathway involved in axon guidance
399 cellular pigmentation
401 antigen processing and presentation of endogenous antigen
402 establishment of pigment granule localization
403 platelet dense granule organization
234 Arp2/3 complex-mediated actin nucleation
668 establishment of epithelial cell polarity
670 pseudopodium organization
671 fucosylation
672 histone H3-K9 trimethylation
673 establishment of epithelial cell apical/basal polarity
349 protein hydroxylation
350 polyol catabolic process
556 Golgi to plasma membrane transport
186 cortical actin cytoskeleton organization
558 membrane protein ectodomain proteolysis
308 protein localization to Golgi apparatus
560 positive regulation by host of viral process
561 negative regulation of type I interferon-mediated signaling pathway
470 mitochondrial outer membrane permeabilization
108 mitochondrial respiratory chain complex I assembly
132 positive regulation of stress fiber assembly
1026 GMP metabolic process
407 nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway
1031 peptide antigen assembly with MHC class II protein complex
1032 mitochondrial electron transport, ubiquinol to cytochrome c
1033 cobalamin metabolic process
1034 positive regulation of pseudopodium assembly
1035 protein insertion into mitochondrial outer membrane
1036 smoothened signaling pathway involved in dorsal/ventral neural tube patterning
1037 histone H3 deacetylation
1038 negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway
1039 regulation of mitophagy
1040 positive regulation of autophagy of mitochondrion
1041 regulation of RNA binding
192 lactation
788 positive regulation of establishment of protein localization
358 establishment of mitochondrion localization
800 positive regulation of ubiquitin-dependent protein catabolic process
825 regulation of membrane permeability
317 vesicle targeting, to, from or within Golgi
318 protein localization to centrosome
826 cellular copper ion homeostasis
681 RIG-I signaling pathway
684 regulation of fatty acid beta-oxidation
685 negative regulation of translational initiation
686 lipid import into cell
491 phosphorus metabolic process
199 Rac protein signal transduction
569 purine nucleoside monophosphate biosynthetic process
570 histone H2A monoubiquitination
571 peroxisomal transport
486 positive regulation of response to endoplasmic reticulum stress
487 peroxisome organization
489 COPII vesicle coating
490 regulation of establishment of cell polarity
72 negative regulation of protein ubiquitination
412 protein quality control for misfolded or incompletely synthesized proteins
413 receptor catabolic process
414 regulation of cytoplasmic transport
362 hippo signaling
43 purine ribonucleoside triphosphate biosynthetic process
279 TOR signaling
249 endosome transport via multivesicular body sorting pathway
166 organelle localization
797 Golgi vesicle transport
1051 stress fiber assembly
835 organelle localization by membrane tethering
323 cellular response to amino acid starvation
226 amino acid activation
375 acetyl-CoA metabolic process
420 cotranslational protein targeting to membrane
421 regulation of mitochondrial gene expression
422 regulation of oxidative stress-induced neuron death
694 ribosomal large subunit assembly
495 negative regulation of defense response to virus
578 negative regulation of keratinocyte proliferation
579 protein localization to endosome
696 negative regulation of release of cytochrome c from mitochondria
838 translational termination
839 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
840 response to sterol depletion
841 activation of NF-kappaB-inducing kinase activity
842 small regulatory ncRNA 3'-end processing
843 cellular response to exogenous dsRNA
844 lamellipodium morphogenesis
845 regulation of chemokine (C-X-C motif) ligand 2 production
846 negative regulation of anoikis
1059 glutathione biosynthetic process
1060 positive regulation of triglyceride biosynthetic process
1061 SREBP signaling pathway
1062 negative regulation of tyrosine phosphorylation of STAT protein
1063 cytoplasmic sequestering of transcription factor
1064 glycosphingolipid catabolic process
1065 Golgi inheritance
1066 protein heterotetramerization
1067 negative regulation of androgen receptor signaling pathway
1068 peptidyl-serine dephosphorylation
1069 tRNA 5'-end processing
1070 positive regulation of ruffle assembly
1071 positive regulation of telomerase RNA localization to Cajal body
22 positive regulation of I-kappaB kinase/NF-kappaB signaling
124 positive regulation of autophagy
70 ATP synthesis coupled electron transport
228 epidermal growth factor receptor signaling pathway
262 mitochondrial outer membrane permeabilization involved in programmed cell death
263 negative regulation of response to endoplasmic reticulum stress
380 protein localization to microtubule cytoskeleton
84 endosome organization
427 positive regulation of ubiquitin-protein transferase activity
62 mitochondrial translation
224 endosomal transport
503 peripheral nervous system axon ensheathment
504 monoubiquitinated histone H2A deubiquitination
505 regulation of cytoplasmic translation
592 viral budding
593 mitochondrion transport along microtubule
712 mitophagy
714 negative regulation of histone methylation
715 SNARE complex assembly
716 extracellular vesicle biogenesis
103 protein monoubiquitination
51 ATP metabolic process
110 regulation of ERBB signaling pathway
52 nucleoside triphosphate biosynthetic process
330 Golgi to plasma membrane protein transport
331 integrated stress response signaling
858 tRNA wobble base modification
859 glycerol metabolic process
860 N-glycan processing
861 exosomal secretion
1073 nuclear-transcribed mRNA catabolic process
430 regulation of protein targeting
1084 anoikis
435 positive regulation of telomere maintenance via telomerase
436 monoubiquitinated protein deubiquitination
1085 MHC protein complex assembly
1086 oligopeptide transport
1087 protein O-linked mannosylation
1088 intraciliary anterograde transport
1089 protein alpha-1,2-demannosylation
1090 regulation of DNA strand elongation
1091 establishment of protein localization to telomere
1092 epithelial cell-cell adhesion
1093 negative regulation of cilium assembly
1094 regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
515 mitochondrial genome maintenance
516 viral protein processing
517 multivesicular body assembly
297 positive regulation of pattern recognition receptor signaling pathway
377 ribosome biogenesis
601 protein targeting to lysosome
602 positive regulation of protein targeting to membrane
386 regulation of actin nucleation
719 intra-Golgi vesicle-mediated transport
722 cellular response to growth hormone stimulus
440 late endosome to vacuole transport
300 intracellular lipid transport
301 cellular response to osmotic stress
105 mitochondrial transmembrane transport
866 establishment of protein localization to plasma membrane
521 early endosome to late endosome transport
872 purine nucleoside monophosphate metabolic process
875 pinocytosis
876 regulation of nuclease activity
877 myelin assembly
604 microtubule nucleation
101 lysosome organization
605 iron-sulfur cluster assembly
1112 magnesium ion transport
1113 protein localization to microtubule
1114 DNA damage response, signal transduction resulting in transcription
1115 anterograde synaptic vesicle transport
1116 positive regulation of type I interferon-mediated signaling pathway
1117 RNA localization to Cajal body
1118 telomerase RNA localization
1119 synaptic vesicle cytoskeletal transport
270 regulation of lamellipodium organization
732 cleavage involved in rRNA processing
733 negative regulation of microtubule depolymerization
734 antigen processing and presentation of exogenous peptide antigen via MHC class II
735 cerebellar Purkinje cell layer development
218 cytoplasmic microtubule organization
528 positive regulation of exocytosis
532 negative regulation of GTPase activity
305 autophagosome maturation
307 negative regulation of TOR signaling
244 positive regulation of protein localization to plasma membrane
197 positive regulation of telomere maintenance
34 aerobic respiration
114 cellular response to topologically incorrect protein
152 protein autoubiquitination
873 movement in host
137 mitochondrial transport
608 ER-nucleus signaling pathway
344 protein destabilization
447 inner mitochondrial membrane organization
448 pigment granule organization
610 Schwann cell development
611 placenta blood vessel development
612 positive regulation of protein targeting to mitochondrion
887 MyD88-dependent toll-like receptor signaling pathway
888 microvillus organization
889 regulation of membrane protein ectodomain proteolysis
313 positive regulation of actin filament polymerization
391 cellular response to ionizing radiation
392 histone deubiquitination
393 regulation of DNA-templated transcription in response to stress
394 regulation of autophagosome assembly
272 regulation of mitochondrial membrane potential
730 tRNA aminoacylation for protein translation
737 histone demethylation
738 intracellular cholesterol transport
126 neural tube closure
442 JNK cascade
553 positive regulation of protein metabolic process
1097 NADP metabolic process
1098 vesicle docking
1106 regulation of transcription involved in G1/S transition of mitotic cell cycle
1107 mitochondrial electron transport, cytochrome c to oxygen
1108 aspartate family amino acid biosynthetic process
1109 regulation of ARF protein signal transduction
1110 positive regulation of vacuole organization
1111 positive regulation of glycolytic process
54 actin filament bundle assembly
390 selective autophagy
138 regulation of actin filament organization
273 positive regulation of macroautophagy
27 purine nucleoside triphosphate metabolic process
395 purine nucleotide catabolic process
275 nucleoside bisphosphate biosynthetic process
863 positive regulation of proteolysis involved in protein catabolic process
883 regulation of glycolytic process
535 negative regulation of JNK cascade
884 DNA catabolic process, endonucleolytic
885 microtubule anchoring
886 positive regulation of focal adhesion assembly
63 regulation of mitochondrion organization
312 negative regulation of innate immune response
314 non-motile cilium assembly
731 ruffle assembly
196 Wnt signaling pathway
534 cell redox homeostasis
49 vacuole organization
18 protein transport
248 regulation of cell-substrate junction organization
1083 ribosomal small subunit biogenesis
92 endoplasmic reticulum to Golgi vesicle-mediated transport
1099 positive regulation of interferon-alpha production
1100 negative regulation of Rho protein signal transduction
1101 sphingoid metabolic process
1102 cellular response to misfolded protein
1103 negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator
1104 negative regulation of membrane permeability
396 histone ubiquitination
397 negative regulation of stress-activated protein kinase signaling cascade
874 mRNA polyadenylation
878 dosage compensation by inactivation of X chromosome
879 regulation of lipopolysaccharide-mediated signaling pathway
880 stress granule assembly
881 regulation of nucleotide-excision repair
882 regulation of double-strand break repair via nonhomologous end joining
724 vesicle targeting
247 necrotic cell death
736 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
606 regulation of focal adhesion assembly
609 protein K63-linked deubiquitination
533 cellular response to epidermal growth factor stimulus
130 neural tube formation
311 regulation of translational initiation
246 pyridine nucleotide metabolic process
201 retrograde transport, endosome to Golgi
171 mitochondrion disassembly
75 regulation of cell shape
39 cellular response to DNA damage stimulus
507 phospholipid biosynthetic process
179 monosaccharide biosynthetic process
444 ribosomal large subunit biogenesis
526 phosphatidylinositol phosphate biosynthetic process
857 gluconeogenesis
527 regulation of tumor necrosis factor-mediated signaling pathway
315 positive regulation of response to cytokine stimulus
347 antigen processing and presentation of peptide antigen
449 myeloid leukocyte cytokine production
450 regulation of extrinsic apoptotic signaling pathway via death domain receptors
607 positive regulation of DNA replication
727 regulation of programmed necrotic cell death
728 protein K48-linked deubiquitination
869 heme biosynthetic process
870 interleukin-1-mediated signaling pathway
871 cellular response to gamma radiation
33 ribonucleoside triphosphate metabolic process
1076 phosphatidylserine metabolic process
1077 ether metabolic process
1078 positive regulation of natural killer cell activation
1079 negative regulation of T cell receptor signaling pathway
295 regulation of GTPase activity
28 intracellular transport
41 regulation of protein modification by small protein conjugation or removal
346 cellular response to heat
149 regulation of small GTPase mediated signal transduction
2 cellular nitrogen compound biosynthetic process
446 positive regulation of membrane permeability
106 positive regulation of cell projection organization
530 regulation of centrosome duplication
531 response to antibiotic
25 intracellular protein transport
603 regulation of mitotic spindle organization
212 mRNA catabolic process
718 establishment of protein localization to mitochondrial membrane
1030 mitochondrial gene expression
853 protein dealkylation
854 lipid droplet organization
855 phosphatidylinositol dephosphorylation
856 centrosome localization
119 positive regulation of translation
1052 intracellular protein transmembrane transport
441 regulation of microtubule polymerization
1053 intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
1056 B cell apoptotic process
1057 telomere maintenance in response to DNA damage
1058 positive regulation of release of cytochrome c from mitochondria
89 positive regulation of NF-kappaB transcription factor activity
522 acylglycerol biosynthetic process
523 regulation of mitochondrial membrane permeability involved in apoptotic process
600 positive regulation of substrate adhesion-dependent cell spreading
711 positive regulation of protein polymerization
44 ribose phosphate biosynthetic process
83 nuclear export
713 quinone metabolic process
506 tumor necrosis factor-mediated signaling pathway
241 positive regulation of apoptotic signaling pathway
188 intrinsic apoptotic signaling pathway
518 negative regulation of I-kappaB kinase/NF-kappaB signaling
847 tetrapyrrole biosynthetic process
82 transport along microtubule
58 positive regulation of protein catabolic process
287 RNA splicing
595 antigen processing and presentation of exogenous antigen
167 carbohydrate catabolic process
1046 cellular component disassembly involved in execution phase of apoptosis
1047 protein K11-linked ubiquitination
104 purine ribonucleotide biosynthetic process
94 regulation of intracellular transport
514 regulation of gluconeogenesis
116 protein targeting
376 protein localization to nucleus
831 dendritic spine development
118 epithelial tube formation
583 alpha-amino acid biosynthetic process
1209 protein modification by small protein conjugation
832 maintenance of protein localization in organelle
833 positive regulation of microtubule polymerization or depolymerization
368 regulation of protein stability
9 cellular macromolecule biosynthetic process
319 macroautophagy
502 establishment or maintenance of apical/basal cell polarity
91 protein localization to plasma membrane
163 positive regulation of supramolecular fiber organization
693 membrane fission
1027 glycoprotein catabolic process
1028 diol metabolic process
582 regulation of filopodium assembly
7 modification-dependent macromolecule catabolic process
73 small GTPase mediated signal transduction
231 positive regulation of cytoskeleton organization
64 ubiquitin-dependent protein catabolic process
830 cytochrome complex assembly
484 dephosphorylation
240 phosphorylation
59 proteasome-mediated ubiquitin-dependent protein catabolic process
687 fatty acid beta-oxidation
645 regulation of protein-containing complex assembly
690 vesicle docking involved in exocytosis
383 circadian regulation of gene expression
208 purine ribonucleoside diphosphate metabolic process
21 nucleobase-containing compound biosynthetic process
492 apoptotic mitochondrial changes
135 response to unfolded protein
258 negative regulation of protein kinase activity
1017 phosphatidic acid biosynthetic process
1018 positive regulation of transforming growth factor beta receptor signaling pathway
379 cellular response to mechanical stimulus
162 mRNA transport
13 protein localization
802 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
35 positive regulation of catabolic process
573 regulation of dendritic spine development
125 monosaccharide metabolic process
676 G1/S transition of mitotic cell cycle
1136 heterocycle biosynthetic process
677 protein targeting to mitochondrion
141 regulation of plasma membrane bounded cell projection assembly
416 activation of cysteine-type endopeptidase activity involved in apoptotic process
324 ATP generation from ADP
325 endocytic recycling
789 positive regulation of glucose metabolic process
790 hexose catabolic process
1014 negative regulation of macroautophagy
1277 deoxyribonucleotide catabolic process
1278 viral release from host cell
1279 entrainment of circadian clock by photoperiod
1280 deoxyribose phosphate catabolic process
1281 lung cell differentiation
360 myelination
513 autophagy
143 ensheathment of neurons
485 histone H4 acetylation
982 cytosolic transport
8 peptide biosynthetic process
316 cellular carbohydrate metabolic process
145 positive regulation of protein modification process
783 regulation of histone deacetylation
784 cellular carbohydrate catabolic process
992 positive regulation of glucose import
993 membrane lipid catabolic process
557 mitochondrial membrane organization
15 proteolysis involved in protein catabolic process
562 transcription elongation by RNA polymerase II promoter
1227 isoprenoid biosynthetic process
1228 cellular metabolic compound salvage
1229 positive regulation of signal transduction by p53 class mediator
87 protein stabilization
973 rRNA metabolic process
86 vesicle localization
639 regulation of macroautophagy
980 mitochondrial respiratory chain complex assembly
277 nucleotide phosphorylation
455 regulation of intrinsic apoptotic signaling pathway
406 positive regulation of cytokine production involved in immune response
644 nucleotide-excision repair
985 telomere capping
1213 regulation of reactive oxygen species metabolic process
235 DNA-templated transcription elongation
551 positive regulation of viral process
552 axonal transport
1216 androgen receptor signaling pathway
122 cellular response to oxidative stress
765 ribonucleotide catabolic process
766 regulation of myelination
767 thymus development
768 regulation of cell cycle checkpoint
356 cell-substrate junction assembly
215 protein deacylation
457 endosome to lysosome transport
971 regulation of stress fiber assembly
80 purine-containing compound biosynthetic process
1080 regulation of biosynthetic process
979 regulation of protein localization to cell surface
48 energy derivation by oxidation of organic compounds
213 monocarboxylic acid catabolic process
214 regulation of protein localization to cell periphery
133 myeloid cell homeostasis
53 cellular macromolecule catabolic process
760 peptidyl-cysteine modification
146 protein modification by small protein removal
637 ribonucleoside monophosphate metabolic process
1197 telomere maintenance via telomerase
237 activation of GTPase activity
1202 nucleobase metabolic process
1203 cerebellar cortex morphogenesis
1204 negative regulation of type I interferon production
1205 response to fluid shear stress
1206 positive regulation of erythrocyte differentiation
1207 positive regulation of telomerase activity
160 proton transmembrane transport
966 establishment of protein localization to vacuole
299 regulation of DNA-templated transcription elongation
968 positive regulation of JUN kinase activity
233 organelle fusion
630 regulation of telomere maintenance via telomere lengthening
334 pyruvate metabolic process
206 Golgi organization
585 regulation of cell morphogenesis
66 negative regulation of transferase activity
404 establishment of protein localization to organelle
445 negative regulation of protein-containing complex disassembly
537 regulation of intracellular steroid hormone receptor signaling pathway
627 protein sumoylation
743 cellular response to glucose starvation
911 vesicle transport along microtubule
912 acyl-CoA biosynthetic process
1190 lens fiber cell differentiation
1191 cellular response to cadmium ion
168 rRNA processing
96 protein autophosphorylation
148 peptidyl-serine phosphorylation
625 endothelial cell development
902 endoplasmic reticulum unfolded protein response
384 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
903 positive regulation of stem cell population maintenance
1149 nucleotide transport
1150 positive regulation of epidermal growth factor receptor signaling pathway
409 positive regulation of protein-containing complex assembly
425 positive regulation of double-strand break repair
36 ribonucleotide metabolic process
739 protein homotetramerization
501 positive regulation of axonogenesis
897 positive regulation of protein dephosphorylation
898 developmental pigmentation
364 actin cytoskeleton reorganization
345 nucleocytoplasmic transport
497 dendritic spine organization
157 glycerophospholipid biosynthetic process
726 mRNA stabilization
1138 DNA synthesis involved in DNA repair
1139 regulation of fibroblast migration
1140 positive regulation of protein import into nucleus
1141 toxin transport
891 post-translational protein modification
158 regulation of RNA splicing
892 viral transcription
787 I-kappaB kinase/NF-kappaB signaling
410 cellular response to hydrogen peroxide
1130 clathrin-dependent endocytosis
20 regulation of cellular response to stress
471 cellular response to insulin stimulus
1131 toll-like receptor 4 signaling pathway
862 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
867 transcription by RNA polymerase III
868 maturation of SSU-rRNA
692 negative regulation of actin filament polymerization
185 establishment of RNA localization
191 regulation of protein localization
1095 post-Golgi vesicle-mediated transport
352 peptidyl-threonine phosphorylation
1120 lamellipodium assembly
405 regulation of cell morphogenesis involved in differentiation
567 cellular response to type I interferon
1122 protein targeting to ER
1123 semaphorin-plexin signaling pathway
203 nucleic acid transport
19 localization within membrane
337 lipid oxidation
113 establishment or maintenance of cell polarity
1055 histone deacetylation
187 establishment of protein localization to membrane
785 actin filament polymerization
67 purine nucleotide metabolic process
539 glucose metabolic process
1074 centriole assembly
675 positive regulation of reactive oxygen species metabolic process
251 negative regulation of protein-containing complex assembly
452 thioester metabolic process
159 tRNA metabolic process
387 ceramide metabolic process
190 regulation of protein localization to membrane
1042 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
1043 positive regulation of TOR signaling
1044 regulation of cellular respiration
1045 regulation of TORC1 signaling
139 response to starvation
281 centrosome cycle
123 cellular response to nutrient levels
50 cellular metabolic process
321 protein import into nucleus
443 cellular oxidant detoxification
90 nucleotide biosynthetic process
169 regulation of proteasomal protein catabolic process
1020 intermembrane lipid transfer
1021 positive regulation of extrinsic apoptotic signaling pathway
769 bone resorption
770 ncRNA transcription
536 cellular response to acid chemical
31 negative regulation of protein modification process
1013 porphyrin-containing compound metabolic process
849 nucleobase-containing small molecule metabolic process
382 regulation of autophagy
757 substrate adhesion-dependent cell spreading
1 macromolecule localization
55 nucleoside phosphate metabolic process
989 intracellular estrogen receptor signaling pathway
336 regulation of cysteine-type endopeptidase activity involved in apoptotic process
598 modulation by host of symbiont process
252 regulation of actin polymerization or depolymerization
342 regulation of cytoskeleton organization
580 erythrocyte differentiation
76 nucleobase-containing compound catabolic process
584 ubiquitin-dependent ERAD pathway
333 nucleoside diphosphate metabolic process
574 microtubule polymerization or depolymerization
204 protein dephosphorylation
969 actin filament depolymerization
207 regulation of DNA repair
170 cellular biosynthetic process
57 regulation of actin filament-based process
723 protein localization to endoplasmic reticulum
1231 regulation of p38MAPK cascade
566 endoplasmic reticulum organization
115 regulation of cellular catabolic process
1215 negative regulation of cold-induced thermogenesis
150 ribonucleoprotein complex subunit organization
682 negative regulation of RNA catabolic process
1195 positive regulation of transcription elongation by RNA polymerase II
1196 negative regulation of reactive oxygen species metabolic process
296 morphogenesis of embryonic epithelium
357 steroid hormone mediated signaling pathway
1151 negative regulation of protein serine/threonine kinase activity
144 organic acid catabolic process
288 positive regulation of response to DNA damage stimulus
850 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
851 regulation of lipid kinase activity
852 mammary gland epithelium development
1187 positive regulation of regulated secretory pathway
643 regulation of protein depolymerization
348 positive regulation of protein localization
85 catabolic process
795 nucleoside phosphate catabolic process
142 cellular response to external stimulus
472 regulation of response to cytokine stimulus
1133 response to ischemia
320 regulation of microtubule cytoskeleton organization
1124 positive regulation of T cell mediated immunity
1125 negative regulation of viral genome replication
1126 T cell apoptotic process
749 extrinsic apoptotic signaling pathway
763 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
764 carbohydrate derivative transport
454 cellular response to toxic substance
1075 insulin secretion involved in cellular response to glucose stimulus
1029 negative regulation of intrinsic apoptotic signaling pathway
155 response to tumor necrosis factor
747 reactive nitrogen species metabolic process
972 protein-containing complex disassembly
438 ribonucleoside bisphosphate metabolic process
439 purine nucleoside bisphosphate metabolic process
725 signal transduction by p53 class mediator
742 mitotic cytokinesis
225 response to reactive oxygen species
68 positive regulation of DNA-templated transcription
987 positive regulation of NIK/NF-kappaB signaling
519 Rho protein signal transduction
688 regulation of purine nucleotide metabolic process
978 chaperone-mediated protein folding
678 regulation of cellular response to oxidative stress
642 negative regulation of cytoskeleton organization
905 protein O-linked glycosylation
717 positive regulation of macromolecule biosynthetic process
473 spindle assembly
900 nitric oxide biosynthetic process
355 regulation of organelle assembly
974 mitochondrion organization
95 negative regulation of phosphorylation
772 regulation of protein polymerization
837 alternative mRNA splicing, via spliceosome
326 regulation of Ras protein signal transduction
1234 histone H3 acetylation
829 myeloid cell development
1237 DNA damage response, signal transduction by p53 class mediator
1239 sulfur compound transport
791 positive regulation of protein binding
306 cellular lipid catabolic process
774 lipid storage
176 regulation of cell cycle
679 organic substance biosynthetic process
1222 platelet-derived growth factor receptor signaling pathway
1223 negative regulation of small GTPase mediated signal transduction
198 phosphate-containing compound metabolic process
1201 negative regulation of MAP kinase activity
164 positive regulation of organelle organization
520 phosphatidylinositol metabolic process
99 cellular response to stress
751 negative regulation of mRNA metabolic process
1143 autophagosome assembly
1189 negative regulation of intracellular transport
353 ribonucleoprotein complex biogenesis
493 regulation of protein localization to nucleus
341 membrane fusion
180 protein acylation
990 organophosphate catabolic process
408 cellular amide metabolic process
636 integrin-mediated signaling pathway
398 negative regulation of cellular catabolic process
591 insulin receptor signaling pathway
351 regulation of cellular component size
1241 mRNA metabolic process
385 cellular response to oxygen levels
895 positive regulation of protein ubiquitination
906 lysosome localization
129 organophosphate metabolic process
255 positive regulation of proteolysis
494 regulation of cell projection organization
836 maintenance of protein location
172 cell cycle phase transition
626 response to endoplasmic reticulum stress
46 protein modification process
437 actin filament organization
680 regulation of protein binding
683 regulation of mRNA stability
1214 macromolecule biosynthetic process
238 regulation of chromosome organization
378 internal peptidyl-lysine acetylation
596 stem cell population maintenance
597 sulfur compound biosynthetic process
220 protein localization to organelle
559 transition metal ion homeostasis
1128 regulation of nucleocytoplasmic transport
1148 viral genome replication
1142 negative regulation of response to DNA damage stimulus
1132 regulation of toll-like receptor signaling pathway
424 positive regulation of endopeptidase activity
411 protein-containing complex localization
310 glycosylation
111 negative regulation of phosphorus metabolic process
147 carbohydrate derivative metabolic process
798 glycolipid metabolic process
799 cellular response to ketone
786 RNA destabilization
100 protein ubiquitination
112 protein phosphorylation
1129 membrane lipid metabolic process
1137 vesicle fusion
429 negative regulation of cell projection organization
565 regulation of cellular component biogenesis
1121 RNA 3'-end processing
929 positive regulation of histone modification
977 cell death in response to oxidative stress
1127 RNA methylation
136 membrane organization
264 regulation of neuron projection development
117 protein metabolic process
37 positive regulation of cellular metabolic process
508 telomere organization
628 regulation of cellular carbohydrate metabolic process
710 G2/M transition of mitotic cell cycle
720 lipoprotein metabolic process
740 nucleus organization
175 in utero embryonic development
30 organelle organization
865 regulation of circadian rhythm
893 leukocyte apoptotic process
1096 lipid modification
901 cellular response to virus
140 organic substance catabolic process
988 positive regulation of mRNA catabolic process
5 cellular component organization or biogenesis
265 positive regulation of cellular component biogenesis
1082 negative regulation of extrinsic apoptotic signaling pathway
1135 positive regulation of endocytosis
266 biological process involved in symbiotic interaction
1146 regulation of axon extension
81 cell cycle
465 intracellular receptor signaling pathway
77 organonitrogen compound biosynthetic process
1208 cellular response to UV
1238 protein lipidation
1240 regulation of intracellular pH
796 protein catabolic process
153 cell death
695 regulation of stress-activated MAPK cascade
721 cellular response to hypoxia
781 protein glycosylation
575 mRNA processing
750 regulation of viral life cycle
827 regulation of dephosphorylation
369 defense response to virus
986 DNA damage checkpoint signaling
499 regulation of protein transport
24 regulation of macromolecule biosynthetic process
1012 cellular monovalent inorganic cation homeostasis
32 peptidyl-amino acid modification
1188 cellular response to alcohol
302 plasma membrane bounded cell projection assembly
1220 positive regulation of JNK cascade
1221 regulation of protein tyrosine kinase activity
239 apoptotic process
388 organonitrogen compound metabolic process
1016 regulation of DNA biosynthetic process
227 glycerolipid metabolic process
243 cilium organization
222 carboxylic acid metabolic process
640 actin cytoskeleton organization
274 cellular response to peptide
10 regulation of nucleic acid-templated transcription
572 regulation of mRNA metabolic process
211 cell division
151 regulation of cellular macromolecule biosynthetic process
12 regulation of RNA metabolic process
594 cellular component disassembly
984 positive regulation of protein transport
60 RNA biosynthetic process
107 regulation of transcription by RNA polymerase II
11 regulation of cellular biosynthetic process
1015 regulation of apoptotic signaling pathway
71 negative regulation of transcription by RNA polymerase II
200 small molecule biosynthetic process
1210 response to amino acid
828 positive regulation of cell growth
280 establishment of organelle localization
864 microtubule cytoskeleton organization involved in mitosis
970 peptide metabolic process
745 cytokinesis
746 regulation of G1/S transition of mitotic cell cycle
74 DNA-templated transcription
381 RNA splicing, via transesterification reactions
16 regulation of primary metabolic process
554 DNA replication
242 chromatin organization
282 carbohydrate derivative biosynthetic process
26 positive regulation of nucleobase-containing compound metabolic process
641 positive regulation of protein serine/threonine kinase activity
674 neurogenesis
1198 gland morphogenesis
253 regulation of DNA-binding transcription factor activity
65 cellular macromolecule metabolic process
909 negative regulation of binding
29 regulation of nitrogen compound metabolic process
131 organic acid metabolic process
210 regulation of mitotic cell cycle
691 cellular amino acid metabolic process
981 epigenetic regulation of gene expression
205 regulation of cellular amide metabolic process
294 immune response-regulating signaling pathway
426 carboxylic acid biosynthetic process
896 regulation of cell size
1192 positive regulation of stress-activated protein kinase signaling cascade
56 negative regulation of RNA biosynthetic process
1211 histone lysine methylation
165 regulation of cell death
782 negative regulation of organelle organization
47 negative regulation of nucleobase-containing compound metabolic process
193 positive regulation of catalytic activity
638 nucleic acid phosphodiester bond hydrolysis
1022 positive regulation of GTPase activity
4 cellular aromatic compound metabolic process
576 negative regulation of cell cycle phase transition
428 organonitrogen compound catabolic process
1194 dendrite morphogenesis
1054 entry into host
42 positive regulation of RNA biosynthetic process
744 cellular response to abiotic stimulus
1105 positive regulation of neuron projection development
741 regulation of cellular metabolic process
564 DNA repair
794 cell-cell junction organization
6 organic cyclic compound metabolic process
758 regulation of cell-substrate adhesion
209 cellular response to hormone stimulus
400 regulation of protein kinase activity
217 regulation of transferase activity
1200 multicellular organism growth
563 regulation of response to biotic stimulus
1236 regulation of peptidyl-serine phosphorylation
894 protein methylation
271 positive regulation of programmed cell death
327 positive regulation of kinase activity
45 primary metabolic process
456 peptidyl-tyrosine phosphorylation
1023 histone modification
17 establishment of localization
803 mRNA splicing, via spliceosome
801 protein complex oligomerization
1019 ncRNA processing
834 vesicle-mediated transport
14 positive regulation of biological process
177 regulation of catalytic activity
1232 tissue remodeling
1048 myeloid leukocyte differentiation
1049 protein kinase B signaling
156 regulation of cellular component organization
322 organelle assembly
276 cellular response to nitrogen compound
771 positive regulation of cell development
1219 negative regulation of protein localization
669 methylation
93 negative regulation of biosynthetic process
762 regulation of small molecule metabolic process
1050 neuron apoptotic process
759 negative regulation of DNA-templated transcription
335 embryo development ending in birth or egg hatching
709 fatty acid metabolic process
23 nucleic acid metabolic process
689 positive regulation of molecular function
245 plasma membrane bounded cell projection organization
488 regulation of vesicle-mediated transport
577 regulation of apoptotic process
629 wound healing
967 positive regulation of hydrolase activity
975 response to decreased oxygen levels
183 regulation of protein metabolic process
1145 regulation of cell growth
286 regulation of intracellular signal transduction
899 regulation of Wnt signaling pathway
1233 negative regulation of intracellular signal transduction
219 neuron development
550 response to inorganic substance
568 mitotic cell cycle process
102 regulation of response to stimulus
173 negative regulation of cell communication
1217 response to transforming growth factor beta
529 cell projection morphogenesis
184 cellular localization
994 protein localization to extracellular region
309 immune system development
189 negative regulation of signaling
97 negative regulation of cellular process
793 response to radiation
121 regulation of signaling
1226 canonical Wnt signaling pathway
976 negative regulation of cell cycle
1081 alcohol metabolic process
363 regulation of phosphorus metabolic process
389 growth
134 regulation of cell communication
729 cellular component assembly
1193 glycoprotein metabolic process
1242 microtubule cytoskeleton organization
354 negative regulation of cell death
890 endocytosis
930 lipid biosynthetic process
524 protein-containing complex assembly
1225 protein maturation
415 response to organonitrogen compound
748 cell morphogenesis involved in differentiation
431 hemopoiesis
1024 response to peptide hormone
1235 response to steroid hormone
332 positive regulation of transcription by RNA polymerase II
498 regulation of phosphorylation
1230 protein secretion
624 regulation of cell cycle process
496 positive regulation of phosphate metabolic process
599 cellular component morphogenesis
983 response to extracellular stimulus
1025 axon development
1144 neuron projection morphogenesis
1218 positive regulation of cell adhesion
343 homeostatic process
1134 cellular response to organic cyclic compound
708 negative regulation of nitrogen compound metabolic process
1212 positive regulation of cell migration
525 positive regulation of signal transduction
1072 positive regulation of protein phosphorylation
555 negative regulation of response to stimulus
423 regulation of localization
1224 cellular response to cytokine stimulus
1199 negative regulation of apoptotic process
824 generation of neurons
1186 enzyme-linked receptor protein signaling pathway
761 regulation of developmental process
904 regulation of gene expressionredgo <- goresults[goresults\(Size >= 3 & goresults\)Size <= 300 & goresults$Count >= 29, ]
In the given context, “Size” refers to the total number of genes associated with a specific Gene Ontology Biological Process ID (GOBPID). It indicates the number of genes in the dataset that are related to the biological process represented by the GOBPID.
On the other hand, “Count” represents the number of genes within the dataset that were found to be associated with the given GOBPID. It indicates the number of genes in the dataset that were experimentally observed or predicted to be involved in the biological process represented by the GOBPID.
************************ add more constrictions to the filtering!!!!!!!
geneIDs <- geneIdsByCategory(hgOverCond)[goresults$GOBPID]
geneSYMs <- sapply(geneIDs, function(id) select(org.Hs.eg.db, columns="SYMBOL", key=id, keytype="ENTREZID")$SYMBOL)
geneSYMs <- sapply(geneSYMs, paste, collapse=", ")
goresults <- cbind(goresults, Genes=geneSYMs)
rownames(goresults) <- 1:nrow(goresults)
ktab <- kable(goresults, "html", caption="GO results.")
ktab <- kable_styling(ktab, bootstrap_options=c("stripped", "hover", "responsive"), fixed_thead=TRUE)
save_kable(ktab, file="../doc/goresults_no3.html", self_contained=TRUE)goresults
GOBPID Pvalue OddsRatio ExpCount Count Size
1 GO:0019080 4.372384e-06 24.132498 6.786241 16 17
2 GO:0001732 1.066506e-05 22.541471 6.400530 15 16
3 GO:0032486 1.370322e-04 18.025701 5.200430 12 13
4 GO:1903265 1.370322e-04 18.025701 5.200430 12 13
5 GO:0046931 7.289539e-04 15.029038 4.398299 10 11
6 GO:0032790 7.321902e-04 15.017268 4.400364 10 11
7 GO:0033869 7.321902e-04 15.017268 4.400364 10 11
8 GO:0090527 7.321902e-04 15.017268 4.400364 10 11
9 GO:0009113 1.674598e-03 13.513674 4.000331 9 10
10 GO:0060397 1.674598e-03 13.513674 4.000331 9 10
11 GO:0070544 1.674598e-03 13.513674 4.000331 9 10
12 GO:0071233 1.674598e-03 13.513674 4.000331 9 10
13 GO:0090557 1.674598e-03 13.513674 4.000331 9 10
14 GO:0000301 3.796011e-03 12.010496 3.600298 8 9
15 GO:0000467 3.796011e-03 12.010496 3.600298 8 9
16 GO:0006012 3.796011e-03 12.010496 3.600298 8 9
17 GO:0007220 3.796011e-03 12.010496 3.600298 8 9
18 GO:0032287 3.796011e-03 12.010496 3.600298 8 9
19 GO:0072344 3.796011e-03 12.010496 3.600298 8 9
20 GO:0140627 3.796011e-03 12.010496 3.600298 8 9
21 GO:0046825 8.425789e-03 10.535383 3.195226 7 8
22 GO:0006369 8.512085e-03 10.507733 3.200265 7 8
23 GO:0010807 8.512085e-03 10.507733 3.200265 7 8
24 GO:0017038 8.512085e-03 10.507733 3.200265 7 8
25 GO:0043634 8.512085e-03 10.507733 3.200265 7 8
26 GO:0048227 8.512085e-03 10.507733 3.200265 7 8
27 GO:0051683 8.512085e-03 10.507733 3.200265 7 8
28 GO:0090063 8.512085e-03 10.507733 3.200265 7 8
29 GO:0098885 8.512085e-03 10.507733 3.200265 7 8
30 GO:2000586 8.512085e-03 10.507733 3.200265 7 8
31 GO:2000643 8.512085e-03 10.507733 3.200265 7 8
32 GO:0150105 2.760942e-04 9.772476 5.997516 13 15
33 GO:0071243 2.763651e-04 9.771124 5.998013 13 15
34 GO:0019885 2.777230e-04 9.764373 6.000497 13 15
35 GO:0072655 1.846757e-02 9.058988 2.790280 6 7
36 GO:1904925 6.065864e-04 9.012022 5.600464 12 14
37 GO:0006166 1.883163e-02 9.005385 2.800232 6 7
38 GO:0007221 1.883163e-02 9.005385 2.800232 6 7
39 GO:0008635 1.883163e-02 9.005385 2.800232 6 7
40 GO:0019673 1.883163e-02 9.005385 2.800232 6 7
41 GO:0034334 1.883163e-02 9.005385 2.800232 6 7
42 GO:0035666 1.883163e-02 9.005385 2.800232 6 7
43 GO:0045054 1.883163e-02 9.005385 2.800232 6 7
44 GO:0046053 1.883163e-02 9.005385 2.800232 6 7
45 GO:0046719 1.883163e-02 9.005385 2.800232 6 7
46 GO:0061002 1.883163e-02 9.005385 2.800232 6 7
47 GO:0070358 1.883163e-02 9.005385 2.800232 6 7
48 GO:0071029 1.883163e-02 9.005385 2.800232 6 7
49 GO:0071035 1.883163e-02 9.005385 2.800232 6 7
50 GO:0071038 1.883163e-02 9.005385 2.800232 6 7
51 GO:0097052 1.883163e-02 9.005385 2.800232 6 7
52 GO:0106035 1.883163e-02 9.005385 2.800232 6 7
53 GO:0150093 1.883163e-02 9.005385 2.800232 6 7
54 GO:1901098 1.883163e-02 9.005385 2.800232 6 7
55 GO:1902231 1.883163e-02 9.005385 2.800232 6 7
56 GO:2000192 1.883163e-02 9.005385 2.800232 6 7
57 GO:0042059 1.302150e-03 8.270167 5.196554 11 13
58 GO:0035331 1.311761e-03 8.259878 5.200430 11 13
59 GO:1990253 1.311761e-03 8.259878 5.200430 11 13
60 GO:0034340 4.066451e-02 7.522910 2.396475 5 6
61 GO:0046827 2.136613e-04 7.512441 7.200596 15 18
62 GO:0036444 2.804342e-03 7.507943 4.800397 10 12
63 GO:0051639 2.804342e-03 7.507943 4.800397 10 12
64 GO:0061795 2.804342e-03 7.507943 4.800397 10 12
65 GO:0015911 4.088882e-02 7.507597 2.399404 5 6
66 GO:0006552 4.094983e-02 7.503451 2.400199 5 6
67 GO:0006566 4.094983e-02 7.503451 2.400199 5 6
68 GO:0019262 4.094983e-02 7.503451 2.400199 5 6
69 GO:0019346 4.094983e-02 7.503451 2.400199 5 6
70 GO:0031581 4.094983e-02 7.503451 2.400199 5 6
71 GO:0032020 4.094983e-02 7.503451 2.400199 5 6
72 GO:0032799 4.094983e-02 7.503451 2.400199 5 6
73 GO:0032803 4.094983e-02 7.503451 2.400199 5 6
74 GO:0034137 4.094983e-02 7.503451 2.400199 5 6
75 GO:0036115 4.094983e-02 7.503451 2.400199 5 6
76 GO:0043456 4.094983e-02 7.503451 2.400199 5 6
77 GO:0044340 4.094983e-02 7.503451 2.400199 5 6
78 GO:0045046 4.094983e-02 7.503451 2.400199 5 6
79 GO:0048205 4.094983e-02 7.503451 2.400199 5 6
80 GO:0051725 4.094983e-02 7.503451 2.400199 5 6
81 GO:0061087 4.094983e-02 7.503451 2.400199 5 6
82 GO:0061734 4.094983e-02 7.503451 2.400199 5 6
83 GO:0070309 4.094983e-02 7.503451 2.400199 5 6
84 GO:0070427 4.094983e-02 7.503451 2.400199 5 6
85 GO:0070842 4.094983e-02 7.503451 2.400199 5 6
86 GO:0086073 4.094983e-02 7.503451 2.400199 5 6
87 GO:0120183 4.094983e-02 7.503451 2.400199 5 6
88 GO:1901289 4.094983e-02 7.503451 2.400199 5 6
89 GO:1901727 4.094983e-02 7.503451 2.400199 5 6
90 GO:1903301 4.094983e-02 7.503451 2.400199 5 6
91 GO:1903371 4.094983e-02 7.503451 2.400199 5 6
92 GO:1903898 4.094983e-02 7.503451 2.400199 5 6
93 GO:1904352 4.094983e-02 7.503451 2.400199 5 6
94 GO:1905684 4.094983e-02 7.503451 2.400199 5 6
95 GO:1990116 4.094983e-02 7.503451 2.400199 5 6
96 GO:2000323 4.094983e-02 7.503451 2.400199 5 6
97 GO:2001286 4.094983e-02 7.503451 2.400199 5 6
98 GO:2001293 4.094983e-02 7.503451 2.400199 5 6
99 GO:0002181 8.499569e-23 7.191080 50.352642 104 126
100 GO:0006744 4.493475e-04 7.010643 6.800563 14 17
101 GO:0046855 4.493475e-04 7.010643 6.800563 14 17
102 GO:1903358 4.493475e-04 7.010643 6.800563 14 17
103 GO:0006413 8.352830e-08 6.911367 15.561949 32 39
104 GO:0015937 5.915433e-03 6.756215 4.400364 9 11
105 GO:0039530 5.915433e-03 6.756215 4.400364 9 11
106 GO:0046504 5.915433e-03 6.756215 4.400364 9 11
107 GO:0051561 5.915433e-03 6.756215 4.400364 9 11
108 GO:0071679 5.915433e-03 6.756215 4.400364 9 11
109 GO:0097384 5.915433e-03 6.756215 4.400364 9 11
110 GO:0007042 1.541591e-04 6.386753 8.400695 17 21
111 GO:0070584 3.151889e-04 6.010231 8.000662 16 20
112 GO:0002084 1.228166e-02 6.004695 4.000331 8 10
113 GO:0010918 1.228166e-02 6.004695 4.000331 8 10
114 GO:0018401 1.228166e-02 6.004695 4.000331 8 10
115 GO:0032261 1.228166e-02 6.004695 4.000331 8 10
116 GO:0033572 1.228166e-02 6.004695 4.000331 8 10
117 GO:0035646 1.228166e-02 6.004695 4.000331 8 10
118 GO:0048194 1.228166e-02 6.004695 4.000331 8 10
119 GO:0048757 1.228166e-02 6.004695 4.000331 8 10
120 GO:0071223 1.228166e-02 6.004695 4.000331 8 10
121 GO:1902237 1.228166e-02 6.004695 4.000331 8 10
122 GO:2000601 1.228166e-02 6.004695 4.000331 8 10
123 GO:0032728 5.549458e-07 5.832364 15.601291 31 39
124 GO:0051438 1.052695e-04 5.722403 9.589917 19 24
125 GO:0097202 6.375333e-04 5.633813 7.600629 15 19
126 GO:0006177 3.897402e-03 5.506079 5.600464 11 14
127 GO:0007175 3.897402e-03 5.506079 5.600464 11 14
128 GO:0035721 3.897402e-03 5.506079 5.600464 11 14
129 GO:0036151 3.897402e-03 5.506079 5.600464 11 14
130 GO:0015986 2.451615e-02 5.283340 3.588037 7 9
131 GO:0022406 2.466192e-02 5.274579 3.591617 7 9
132 GO:0009081 7.284023e-05 5.261621 10.800894 21 27
133 GO:0019068 2.488311e-02 5.261384 3.597016 7 9
134 GO:0006013 2.501834e-02 5.253383 3.600298 7 9
135 GO:0006048 2.501834e-02 5.253383 3.600298 7 9
136 GO:0006072 2.501834e-02 5.253383 3.600298 7 9
137 GO:0006930 2.501834e-02 5.253383 3.600298 7 9
138 GO:0010890 2.501834e-02 5.253383 3.600298 7 9
139 GO:0010994 2.501834e-02 5.253383 3.600298 7 9
140 GO:0015917 2.501834e-02 5.253383 3.600298 7 9
141 GO:0016139 2.501834e-02 5.253383 3.600298 7 9
142 GO:0016559 2.501834e-02 5.253383 3.600298 7 9
143 GO:0045792 2.501834e-02 5.253383 3.600298 7 9
144 GO:0046601 2.501834e-02 5.253383 3.600298 7 9
145 GO:0048845 2.501834e-02 5.253383 3.600298 7 9
146 GO:0051292 2.501834e-02 5.253383 3.600298 7 9
147 GO:0061909 2.501834e-02 5.253383 3.600298 7 9
148 GO:0071225 2.501834e-02 5.253383 3.600298 7 9
149 GO:1900864 2.501834e-02 5.253383 3.600298 7 9
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766 GO:0048255 1.317470e-02 1.836890 24.001987 33 60
767 GO:0000731 3.903878e-02 1.835616 16.001324 22 40
768 GO:0010762 3.903878e-02 1.835616 16.001324 22 40
769 GO:0042307 3.903878e-02 1.835616 16.001324 22 40
770 GO:1901998 3.903878e-02 1.835616 16.001324 22 40
771 GO:0043687 2.195430e-02 1.830051 20.394933 28 51
772 GO:0043484 4.507760e-05 1.829600 70.805861 97 177
773 GO:0019083 2.205763e-02 1.829037 20.401689 28 51
774 GO:0007249 1.800272e-02 1.827246 21.827203 30 55
775 GO:0070301 2.624949e-03 1.826996 37.203079 51 93
776 GO:0072583 3.718915e-02 1.819394 16.794436 23 42
777 GO:0080135 1.328509e-13 1.819284 251.223165 341 629
778 GO:0032869 3.959083e-03 1.818495 34.337889 47 86
779 GO:0034142 3.737094e-02 1.818135 16.801391 23 42
780 GO:0070059 2.099014e-02 1.817191 21.190050 29 53
781 GO:0006383 2.115946e-02 1.815512 21.201755 29 53
782 GO:0030490 2.115946e-02 1.815512 21.201755 29 53
783 GO:0030837 1.216190e-02 1.814025 25.602119 35 64
784 GO:0051236 1.084482e-04 1.813797 65.205397 89 163
785 GO:0032880 1.247903e-04 1.810513 63.604369 87 161
786 GO:0006892 3.480574e-02 1.809102 17.562483 24 44
787 GO:0018107 1.385234e-03 1.806426 44.003642 60 110
788 GO:0030032 3.519683e-02 1.806330 17.578598 24 44
789 GO:0010769 2.341749e-03 1.805754 39.603278 54 99
790 GO:0071357 6.789133e-03 1.804412 30.802550 42 77
791 GO:0045047 3.575742e-02 1.802408 17.601457 24 44
792 GO:0071526 3.575742e-02 1.802408 17.601457 24 44
793 GO:0050657 1.560945e-04 1.796990 64.005298 87 160
794 GO:0051668 7.171862e-14 1.796073 269.222284 363 673
795 GO:0034440 1.283060e-03 1.795015 45.603775 62 114
796 GO:0007163 6.306493e-06 1.794040 93.607748 127 234
797 GO:0016575 3.357660e-02 1.792585 18.374536 25 46
798 GO:0090150 1.176255e-04 1.791714 66.996782 91 168
799 GO:0030041 1.782339e-02 1.789459 23.535143 32 59
800 GO:0006163 1.393470e-07 1.789375 129.957499 176 326
801 GO:0006006 5.677725e-03 1.788998 33.113393 45 83
802 GO:0098534 3.420007e-02 1.788186 18.401523 25 46
803 GO:2000379 1.075584e-02 1.785120 28.002318 38 70
804 GO:0031333 4.048687e-04 1.785017 56.804702 77 142
805 GO:0035383 3.532033e-03 1.784343 37.603112 51 94
806 GO:0006399 4.645437e-05 1.783727 76.806357 104 192
807 GO:0006672 2.003433e-03 1.781518 42.803543 58 107
808 GO:1905475 1.242045e-04 1.775529 68.805695 93 172
809 GO:0031146 3.269976e-02 1.775263 19.201589 26 48
810 GO:0032008 3.269976e-02 1.775263 19.201589 26 48
811 GO:0043457 3.269976e-02 1.775263 19.201589 26 48
812 GO:1903432 3.269976e-02 1.775263 19.201589 26 48
813 GO:0042594 2.396082e-05 1.774829 84.406986 114 211
814 GO:0007098 6.281821e-04 1.773677 54.004470 73 135
815 GO:0031669 1.304614e-05 1.773616 90.370060 122 226
816 GO:0044237 5.475330e-09 1.773410 145.141504 202 445
817 GO:0006606 1.028431e-03 1.772515 49.562967 67 124
818 GO:0098869 3.259838e-03 1.772068 39.203245 53 98
819 GO:0009165 1.280042e-06 1.769959 113.530984 153 284
820 GO:0061136 6.139702e-05 1.763521 77.206390 104 193
821 GO:0120009 3.125664e-02 1.763470 20.001656 27 50
822 GO:2001238 3.125664e-02 1.763470 20.001656 27 50
823 GO:0045453 1.709287e-02 1.761952 25.202086 34 63
824 GO:0098781 1.709287e-02 1.761952 25.202086 34 63
825 GO:0071229 5.320473e-03 1.760894 35.602947 48 89
826 GO:0031400 2.388580e-10 1.755326 205.548932 275 514
827 GO:0006778 2.987029e-02 1.752666 20.801722 28 52
828 GO:0055086 2.066963e-02 1.752436 23.712247 32 60
829 GO:0010506 1.840785e-03 1.749031 46.074554 62 116
830 GO:0034446 1.535680e-02 1.748803 26.771090 36 67
831 GO:0033036 4.052634e-43 1.747067 1172.497048 1509 2931
832 GO:0006753 2.893501e-08 1.744576 158.489286 212 398
833 GO:0030520 2.853991e-02 1.742731 21.601788 29 54
834 GO:0043281 1.282918e-03 1.739467 50.735244 68 127
835 GO:0051851 8.002213e-03 1.735094 33.602781 45 84
836 GO:0008064 4.049063e-04 1.734298 62.805198 84 157
837 GO:0051493 1.320629e-03 1.733084 50.734703 68 128
838 GO:0030218 7.496104e-03 1.732449 34.366704 46 86
839 GO:0034655 3.599560e-07 1.730316 136.530768 182 342
840 GO:0030433 7.665637e-03 1.729391 34.402848 46 86
841 GO:0009132 1.232066e-03 1.728105 52.404338 70 131
842 GO:0031109 7.198721e-03 1.726616 35.170805 47 88
843 GO:0006470 1.593747e-04 1.725178 73.445035 98 184
844 GO:0030042 2.604228e-02 1.725085 23.201920 31 58
845 GO:0006282 1.763987e-04 1.723520 72.747692 97 182
846 GO:0044249 6.191323e-05 1.723253 76.379810 104 213
847 GO:0032970 5.511439e-08 1.720401 160.413277 213 401
848 GO:0070972 1.313115e-02 1.718011 30.002483 40 75
849 GO:1900744 4.816066e-02 1.716421 18.001490 24 45
850 GO:0007029 6.733316e-03 1.713892 36.803046 49 92
851 GO:0031329 6.784600e-06 1.713398 108.152159 144 274
852 GO:0120163 4.586813e-02 1.706748 18.801556 25 47
853 GO:0071826 3.577594e-05 1.702696 93.607748 124 234
854 GO:1902369 1.148927e-02 1.701294 32.402682 43 81
855 GO:0032968 4.368458e-02 1.697921 19.601622 26 49
856 GO:2000378 4.368458e-02 1.697921 19.601622 26 49
857 GO:0016331 7.774691e-04 1.695033 61.205066 81 153
858 GO:0043401 1.476054e-03 1.694162 54.404503 72 136
859 GO:0071901 4.083517e-02 1.694000 20.371745 27 51
860 GO:0016054 2.789182e-05 1.693235 98.408145 130 246
861 GO:2001022 7.030343e-04 1.691362 62.777465 83 157
862 GO:0000288 2.067816e-02 1.690697 27.202252 36 68
863 GO:0043550 2.067816e-02 1.690697 27.202252 36 68
864 GO:0061180 2.067816e-02 1.690697 27.202252 36 68
865 GO:1903307 4.160552e-02 1.689837 20.401689 27 51
866 GO:1901879 1.004554e-02 1.687055 34.802881 46 87
867 GO:1903829 1.358115e-03 1.685449 55.963061 74 141
868 GO:0009056 9.011208e-07 1.685368 134.801584 179 353
869 GO:1901292 1.859930e-02 1.681980 28.780121 38 72
870 GO:0071496 2.736934e-05 1.678458 101.827626 134 255
871 GO:0060759 3.965681e-03 1.677078 45.521710 60 114
872 GO:0002931 3.774286e-02 1.675549 22.001821 29 55
873 GO:0070507 1.003165e-03 1.671659 61.605099 81 154
874 GO:0002711 3.595042e-02 1.669206 22.801887 30 57
875 GO:0045071 3.595042e-02 1.669206 22.801887 30 57
876 GO:0070231 3.595042e-02 1.669206 22.801887 30 57
877 GO:0097191 1.508112e-02 1.667112 31.938588 42 80
878 GO:0043154 1.640111e-02 1.665698 31.202583 41 78
879 GO:1901264 1.640111e-02 1.665698 31.202583 41 78
880 GO:0097237 3.641404e-03 1.663432 48.003973 63 120
881 GO:0035773 3.424483e-02 1.663322 23.601954 31 59
882 GO:2001243 3.190842e-02 1.662079 24.364913 32 61
883 GO:0034612 4.209891e-05 1.661824 100.808344 132 252
884 GO:2001057 1.494795e-02 1.657518 32.802715 43 82
885 GO:0032984 2.625882e-02 1.656158 26.679797 35 67
886 GO:0033875 3.188236e-03 1.655743 50.404172 66 126
887 GO:0034032 3.188236e-03 1.655743 50.404172 66 126
888 GO:0072331 1.313921e-02 1.655237 34.339913 45 86
889 GO:0000281 1.427041e-02 1.653740 33.602781 44 84
890 GO:0000302 2.661265e-04 1.648431 81.206721 106 203
891 GO:0045893 1.601136e-07 1.644965 175.933456 229 444
892 GO:1901224 2.821084e-02 1.643506 26.802218 35 67
893 GO:0007266 5.020551e-03 1.640913 46.772848 61 117
894 GO:1900542 1.185470e-02 1.640378 36.803046 48 92
895 GO:0061077 2.688073e-02 1.639313 27.602285 36 69
896 GO:1900407 1.131796e-02 1.637417 37.603112 49 94
897 GO:0051494 1.002689e-02 1.635461 39.152240 51 98
898 GO:0006493 2.417567e-02 1.633246 29.185484 38 73
899 GO:0010557 1.292267e-02 1.629801 35.993625 47 92
900 GO:0051225 4.074320e-03 1.628449 50.804205 66 127
901 GO:0006809 2.326436e-02 1.628155 30.002483 39 75
902 GO:1902115 1.427157e-03 1.627605 63.916796 83 160
903 GO:0007005 2.644778e-02 1.624532 28.418262 37 72
904 GO:0042326 2.001532e-06 1.622679 152.412615 197 381
905 GO:0032271 1.726586e-02 1.621710 33.897096 44 85
906 GO:0000380 2.014676e-02 1.618747 32.402682 42 81
907 GO:0046578 1.119081e-03 1.617511 68.761989 89 172
908 GO:0043966 4.828704e-02 1.616405 22.376485 29 56
909 GO:0061515 1.920589e-02 1.615931 33.202748 43 83
910 GO:0030330 4.858070e-02 1.615134 22.387008 29 56
911 GO:0072348 4.899755e-02 1.613343 22.401854 29 56
912 GO:0032092 1.831017e-02 1.613256 34.002814 44 85
913 GO:0044242 8.478313e-04 1.611225 73.543021 95 184
914 GO:0019915 1.745734e-02 1.610712 34.802881 45 87
915 GO:0051726 7.940603e-05 1.610328 105.327403 136 265
916 GO:1901576 1.141442e-02 1.610200 36.375904 48 102
917 GO:0048008 4.656628e-02 1.609443 23.201920 30 58
918 GO:0051058 4.656628e-02 1.609443 23.201920 30 58
919 GO:0006796 1.436424e-04 1.608759 94.664849 123 247
920 GO:0043407 4.426389e-02 1.605818 24.001987 31 60
921 GO:0010638 4.968271e-05 1.605014 113.264331 146 285
922 GO:0046488 5.046023e-03 1.604352 51.160374 66 128
923 GO:0033554 2.456622e-06 1.603958 153.258664 198 395
924 GO:1903312 1.513560e-02 1.603777 37.203079 48 93
925 GO:0000045 3.923012e-02 1.602994 25.566718 33 64
926 GO:0032387 4.208287e-02 1.602439 24.802053 32 62
927 GO:0022613 1.400416e-03 1.601075 68.222709 88 172
928 GO:1900180 4.500154e-03 1.597778 53.604437 69 134
929 GO:0061025 1.317708e-03 1.594453 70.805861 91 177
930 GO:0043543 9.883481e-05 1.590653 108.408973 139 271
931 GO:0046434 2.868985e-02 1.589470 30.340171 39 76
932 GO:0043603 2.490890e-03 1.586334 62.120150 80 159
933 GO:0007229 9.441499e-03 1.586291 45.203742 58 113
934 GO:0031330 2.157551e-03 1.585468 65.509091 84 164
935 GO:0008286 7.828608e-03 1.581023 48.404006 62 121
936 GO:0032535 1.380670e-03 1.580873 72.635634 93 182
937 GO:0016071 4.907152e-02 1.579393 24.149550 31 61
938 GO:0071453 1.889049e-03 1.578231 68.805695 88 172
939 GO:0031398 2.274455e-02 1.577699 34.363868 44 86
940 GO:0032418 2.438214e-02 1.576373 33.602781 43 84
941 GO:0019637 1.697071e-05 1.575147 138.520864 177 351
942 GO:0045862 4.090974e-04 1.571577 92.459374 118 232
943 GO:0031344 4.556961e-03 1.570297 57.109370 73 144
944 GO:0045185 2.006789e-02 1.570147 36.803046 47 92
945 GO:0044770 6.899560e-05 1.570040 120.069472 153 301
946 GO:0034976 8.869826e-03 1.565057 48.608686 62 122
947 GO:0036211 3.349286e-09 1.564739 275.651158 351 724
948 GO:0007015 3.166129e-03 1.563831 63.519121 81 160
949 GO:0043393 1.146219e-02 1.561469 45.540585 58 114
950 GO:0043488 1.149984e-02 1.561095 45.546980 58 114
951 GO:0009059 4.571879e-02 1.560989 24.783683 32 67
952 GO:0033044 3.235694e-04 1.558349 100.008278 127 250
953 GO:0018393 1.786968e-03 1.556452 74.006125 94 185
954 GO:0019827 7.900698e-03 1.554296 51.952528 66 130
955 GO:0044272 7.992488e-03 1.553129 51.975588 66 130
956 GO:0033365 2.308635e-04 1.553034 105.418240 134 268
957 GO:0055076 6.412128e-03 1.548639 56.004636 71 140
958 GO:0046822 3.614912e-02 1.547619 30.737852 39 77
959 GO:0019079 4.073494e-02 1.546818 29.173328 37 73
960 GO:2001021 3.906255e-02 1.544246 29.990064 38 75
961 GO:0034121 3.737984e-02 1.542178 30.802550 39 77
962 GO:0010950 2.911414e-03 1.541242 69.605761 88 174
963 GO:0031503 2.654960e-03 1.540591 71.205894 90 178
964 GO:0070085 8.582881e-04 1.536860 90.342576 114 226
965 GO:0010563 5.557059e-06 1.536777 176.414602 222 441
966 GO:1901135 3.144116e-05 1.536312 145.039515 183 367
967 GO:0006664 1.873093e-02 1.532529 42.003477 53 105
968 GO:1901655 1.873093e-02 1.532529 42.003477 53 105
969 GO:0050779 1.784496e-02 1.532054 42.803543 54 107
970 GO:0016567 2.635890e-06 1.522176 197.052516 247 497
971 GO:0006468 5.964003e-06 1.513561 187.127899 234 473
972 GO:0006643 3.685966e-02 1.507279 34.341705 43 86
973 GO:0006906 3.895519e-02 1.506544 33.551697 42 84
974 GO:0031345 3.028006e-03 1.506501 76.806357 96 192
975 GO:0044087 6.694798e-03 1.505768 62.242701 78 158
976 GO:0031123 3.545748e-02 1.505565 35.164991 44 88
977 GO:0031058 2.551971e-02 1.503334 40.803377 51 102
978 GO:0036473 2.680684e-02 1.503264 40.003311 50 100
979 GO:0001510 3.611734e-02 1.502845 35.202914 44 88
980 GO:0061024 2.140934e-05 1.499929 171.054491 213 431
981 GO:0010975 4.784411e-04 1.492914 115.023657 143 288
982 GO:0019538 9.540761e-06 1.491871 182.861473 229 496
983 GO:0031325 5.754904e-10 1.491543 396.068071 489 1014
984 GO:0032200 4.867804e-03 1.489388 72.405993 90 181
985 GO:0010675 8.947217e-03 1.485724 62.005132 77 155
986 GO:0000086 1.246433e-02 1.483337 56.404669 70 141
987 GO:0042157 1.307228e-02 1.482965 55.604602 69 139
988 GO:0006997 1.371085e-02 1.482584 54.804536 68 137
989 GO:0001701 7.531977e-05 1.482404 156.812979 194 392
990 GO:0006996 5.248659e-11 1.480378 460.571429 567 1209
991 GO:0042752 2.113723e-02 1.478693 47.603940 59 119
992 GO:0071887 2.218866e-02 1.478199 46.803874 58 117
993 GO:0030258 3.482410e-02 1.477964 38.714889 48 97
994 GO:0098586 2.329476e-02 1.477691 46.003808 57 115
995 GO:1901575 2.474609e-05 1.475778 179.106985 222 464
996 GO:0061014 2.832967e-02 1.475496 42.803543 53 107
997 GO:0071840 5.073541e-22 1.474290 1223.196511 1459 3228
998 GO:0044089 5.088535e-04 1.473428 121.404629 150 305
999 GO:2001237 3.452022e-02 1.472994 39.603278 49 99
1000 GO:0045807 3.813738e-02 1.471605 38.003146 47 95
1001 GO:0044403 5.237185e-04 1.470898 122.410132 151 306
1002 GO:0030516 4.009485e-02 1.470871 37.203079 46 93
1003 GO:0007049 7.006165e-07 1.470325 265.090042 326 670
1004 GO:0030522 3.877758e-03 1.469718 81.784330 101 205
1005 GO:1901566 4.823417e-07 1.469658 270.221093 333 695
1006 GO:0034644 4.433805e-02 1.469313 35.602947 44 89
1007 GO:0006497 4.867996e-02 1.468847 33.985919 42 85
1008 GO:0051453 4.906470e-02 1.467624 34.002814 42 85
1009 GO:0030163 1.863189e-02 1.467502 50.860059 63 130
1010 GO:0008219 3.972797e-05 1.467133 177.735749 219 451
1011 GO:0032872 1.222589e-02 1.467130 59.955189 74 150
1012 GO:0071456 1.310356e-02 1.464476 59.204900 73 148
1013 GO:0006486 1.753286e-02 1.464318 53.507848 66 134
1014 GO:0006397 7.315362e-03 1.464279 70.549388 87 177
1015 GO:1903900 1.511274e-02 1.462599 56.804702 70 142
1016 GO:0035303 1.919672e-02 1.459140 52.804371 65 132
1017 GO:0051607 1.648099e-03 1.455756 104.223863 128 261
1018 GO:0000077 2.803449e-02 1.453521 46.384632 57 116
1019 GO:0051223 4.777598e-03 1.452725 82.212519 101 207
1020 GO:0010556 6.093549e-13 1.452631 646.824654 782 1659
1021 GO:0030004 2.968836e-02 1.451564 45.603775 56 114
1022 GO:0018193 2.486814e-10 1.449613 491.496320 596 1230
1023 GO:0097306 4.193110e-02 1.443979 40.003311 49 100
1024 GO:0120031 8.236766e-04 1.441735 125.175365 153 315
1025 GO:0046330 4.633524e-02 1.441439 38.403179 47 96
1026 GO:0061097 4.633524e-02 1.441439 38.403179 47 96
1027 GO:0006915 3.237254e-04 1.437900 148.262192 181 376
1028 GO:1901564 2.021580e-03 1.432644 100.377280 124 282
1029 GO:2000278 3.089553e-02 1.430728 48.404006 59 121
1030 GO:0046486 2.690155e-04 1.430380 158.813145 193 397
1031 GO:0044782 3.360887e-04 1.427990 154.812814 188 387
1032 GO:0019752 2.510717e-04 1.427871 161.302204 196 406
1033 GO:0030036 9.927910e-03 1.425774 73.891903 90 187
1034 GO:1901653 5.584892e-04 1.422953 145.143883 176 363
1035 GO:1903506 6.189120e-20 1.418717 1354.112080 1589 3385
1036 GO:1903311 7.136640e-03 1.414713 85.878356 104 215
1037 GO:0051301 2.041316e-04 1.413414 177.188912 214 444
1038 GO:2000112 3.863839e-05 1.412481 223.107565 269 558
1039 GO:0051252 4.684093e-19 1.411905 1318.426664 1545 3317
1040 GO:0022411 7.837123e-03 1.411794 84.256106 102 212
1041 GO:0051222 2.774227e-02 1.410973 54.499555 66 137
1042 GO:0032774 7.867397e-08 1.409106 400.460870 481 1032
1043 GO:0006357 4.255926e-06 1.409070 285.673147 344 728
1044 GO:0031326 3.741539e-19 1.408402 1360.474031 1590 3429
1045 GO:2001233 3.065513e-02 1.407687 52.909899 64 133
1046 GO:0000122 2.138244e-07 1.406930 379.631422 455 949
1047 GO:0044283 1.460218e-04 1.405105 192.733903 232 483
1048 GO:0043200 4.460181e-02 1.401935 45.588674 55 114
1049 GO:0030307 1.920420e-02 1.399566 66.405496 80 166
1050 GO:0051656 6.237797e-04 1.397661 158.145985 190 396
1051 GO:1902850 2.108361e-02 1.396936 64.805364 78 162
1052 GO:0006518 2.619331e-02 1.395375 58.869525 71 150
1053 GO:0000910 1.493899e-02 1.395286 74.006125 89 185
1054 GO:2000045 1.493899e-02 1.395286 74.006125 89 185
1055 GO:0006351 3.525311e-07 1.394153 380.557243 455 982
1056 GO:0000375 1.839003e-03 1.393628 130.810827 157 327
1057 GO:0080090 1.016468e-16 1.392782 1246.095890 1450 3220
1058 GO:0006260 6.235293e-03 1.391568 98.299320 118 246
1059 GO:0006325 3.340499e-04 1.389556 182.100434 218 456
1060 GO:1901137 6.300241e-04 1.387454 164.515891 197 414
1061 GO:0045935 3.215405e-12 1.387338 811.667182 956 2029
1062 GO:0071902 9.949304e-03 1.386994 87.607251 105 219
1063 GO:0022008 1.060769e-02 1.386034 85.918071 103 216
1064 GO:0022612 4.387249e-02 1.385761 49.204073 59 123
1065 GO:0051090 4.081930e-04 1.384138 180.814966 216 452
1066 GO:0044260 1.207553e-07 1.380431 436.965165 520 1145
1067 GO:0051100 2.485258e-02 1.380374 65.205397 78 163
1068 GO:0051171 4.860072e-11 1.379889 738.846872 869 1936
1069 GO:0006082 1.754940e-05 1.379372 283.166937 337 711
1070 GO:0007346 2.027703e-04 1.379352 206.417085 246 516
1071 GO:0006520 1.210662e-02 1.378264 85.343897 102 214
1072 GO:0040029 2.727580e-02 1.377260 63.605265 76 159
1073 GO:0034248 1.651104e-04 1.376163 215.940381 257 540
1074 GO:0002764 7.489124e-04 1.375130 169.614039 202 424
1075 GO:0046394 2.984081e-03 1.373772 128.410629 153 321
1076 GO:0008361 2.286515e-02 1.373292 69.573101 83 174
1077 GO:0070304 4.275127e-02 1.372615 52.804371 63 132
1078 GO:1902679 3.124221e-08 1.371309 518.842945 612 1297
1079 GO:0034968 4.483615e-02 1.370628 52.004304 62 130
1080 GO:0010941 5.274909e-05 1.370467 258.655059 307 651
1081 GO:0010639 1.757403e-02 1.367085 78.972883 94 198
1082 GO:0045934 3.567758e-09 1.366818 614.450858 722 1536
1083 GO:0043085 1.324893e-04 1.365498 233.630838 277 588
1084 GO:0090305 9.681926e-03 1.365029 97.608079 116 244
1085 GO:0043547 3.147916e-02 1.365021 63.038498 75 158
1086 GO:0006725 2.114779e-22 1.360873 2477.405055 2781 6193
1087 GO:1901988 7.357232e-03 1.359355 108.809006 129 272
1088 GO:1901565 3.013052e-03 1.359263 134.676448 160 345
1089 GO:0048813 4.355118e-02 1.359248 55.604602 66 139
1090 GO:0044409 3.347874e-02 1.358948 63.205231 75 158
1091 GO:1902680 1.910801e-09 1.357358 672.055626 786 1680
1092 GO:0071214 1.488435e-02 1.357310 87.714095 104 220
1093 GO:0010976 3.506517e-02 1.357117 62.405165 74 156
1094 GO:0031323 1.396389e-02 1.356269 85.381818 102 231
1095 GO:0006281 6.616396e-03 1.353335 114.916111 136 289
1096 GO:0045216 1.858492e-02 1.353213 82.806854 98 207
1097 GO:1901360 5.661842e-22 1.353073 2573.012968 2876 6432
1098 GO:0010810 1.578309e-02 1.351053 88.807351 105 222
1099 GO:0032870 1.990053e-04 1.350951 237.619668 280 594
1100 GO:0045859 2.184671e-03 1.350945 153.231899 181 385
1101 GO:0051338 2.171455e-04 1.348738 235.946110 278 594
1102 GO:0035264 4.422413e-02 1.347276 58.404834 69 146
1103 GO:0002831 6.583215e-03 1.343289 121.371188 143 304
1104 GO:0033135 4.853957e-02 1.342985 56.804702 67 142
1105 GO:0006479 2.252301e-02 1.339217 82.406821 97 206
1106 GO:0043068 5.433842e-04 1.335815 218.418078 256 546
1107 GO:0033674 1.130788e-03 1.334529 191.947005 225 480
1108 GO:0044238 3.136970e-09 1.333753 794.610290 912 2309
1109 GO:0018108 3.681472e-03 1.329696 152.012582 178 380
1110 GO:0016570 3.150061e-02 1.326579 75.924668 89 191
1111 GO:0051234 4.545012e-15 1.326540 1600.188163 1813 4038
1112 GO:0000398 1.883023e-02 1.321733 96.679268 113 242
1113 GO:0051259 1.880805e-02 1.320239 97.608079 114 244
1114 GO:0034470 3.121879e-02 1.312374 82.385931 96 207
1115 GO:0016192 1.989959e-02 1.311466 98.596329 115 252
1116 GO:0048518 2.440646e-17 1.307345 2472.862321 2736 6194
1117 GO:0050790 8.357178e-05 1.303551 346.942109 401 885
1118 GO:0048771 4.816378e-02 1.300133 71.605927 83 179
1119 GO:0002573 3.289986e-02 1.298857 87.207218 101 218
1120 GO:0043491 3.289986e-02 1.298857 87.207218 101 218
1121 GO:0051128 4.418398e-05 1.298095 389.509871 449 998
1122 GO:0070925 1.049811e-03 1.291630 248.309294 286 625
1123 GO:1901699 5.887738e-04 1.288957 282.823409 325 707
1124 GO:0010720 1.709851e-02 1.287228 122.410132 141 306
1125 GO:1903828 4.632969e-02 1.283274 80.806688 93 202
1126 GO:0032259 1.052071e-02 1.276921 154.412781 177 386
1127 GO:0009890 1.310946e-06 1.275801 676.856023 768 1692
1128 GO:0062012 1.639171e-02 1.274896 134.411125 154 336
1129 GO:0051402 3.299536e-02 1.274287 101.208377 116 253
1130 GO:0045892 1.581440e-02 1.273807 136.101561 156 344
1131 GO:0009792 1.272462e-03 1.273752 269.622317 308 674
1132 GO:0006631 1.241925e-02 1.269822 153.106926 175 383
1133 GO:0090304 5.908704e-13 1.269505 2064.847290 2277 5175
1134 GO:0044093 1.186865e-02 1.269260 154.750841 177 392
1135 GO:0120036 3.524268e-04 1.266255 357.710830 407 904
1136 GO:0060627 4.293001e-03 1.264781 216.817946 247 542
1137 GO:0042981 7.405023e-03 1.263822 186.846163 213 471
1138 GO:0042060 9.189024e-03 1.263380 176.414602 201 441
1139 GO:0051345 2.570133e-02 1.262479 121.882083 139 306
1140 GO:0036293 2.650680e-02 1.260853 122.010099 139 305
1141 GO:0051246 1.054780e-04 1.260791 447.137425 507 1144
1142 GO:0001558 3.964285e-02 1.259785 101.815372 116 255
1143 GO:1902531 6.606841e-04 1.258317 337.433997 383 859
1144 GO:0030111 2.325307e-02 1.256553 132.810993 151 332
1145 GO:1902532 4.826796e-02 1.251456 96.835616 110 244
1146 GO:0048666 2.273707e-04 1.247986 442.836654 499 1107
1147 GO:0010035 6.086803e-03 1.247787 222.818443 252 557
1148 GO:1903047 6.919232e-03 1.244502 219.512831 248 551
1149 GO:0048583 3.197571e-06 1.239364 833.554664 929 2109
1150 GO:0010648 6.920736e-05 1.239210 567.646984 636 1419
1151 GO:0071559 4.592729e-02 1.237477 110.809172 125 277
1152 GO:0048858 5.174448e-03 1.234567 258.021356 290 645
1153 GO:0051641 1.062864e-04 1.232051 552.699409 619 1455
1154 GO:0071692 2.896558e-02 1.230321 146.812152 165 367
1155 GO:0002520 8.577156e-04 1.229168 407.633740 456 1019
1156 GO:0023057 1.213661e-04 1.229055 570.047183 636 1425
1157 GO:0048523 2.331748e-06 1.228453 960.530414 1063 2439
1158 GO:0009314 1.855772e-02 1.227958 180.014900 202 450
1159 GO:0023051 1.100188e-05 1.227138 804.444358 893 2031
1160 GO:0060070 4.737012e-02 1.224627 120.366768 135 301
1161 GO:0045786 2.668495e-02 1.222886 161.613377 181 404
1162 GO:0006066 3.451360e-02 1.221225 145.612052 163 364
1163 GO:0051174 1.628039e-03 1.220054 384.736199 429 968
1164 GO:0040007 2.055773e-03 1.219919 366.830363 409 917
1165 GO:0010646 1.989956e-05 1.219641 801.383786 887 2024
1166 GO:0022607 1.322786e-02 1.219457 213.390914 239 555
1167 GO:0009100 4.346806e-02 1.219428 131.377727 147 329
1168 GO:0000226 4.943521e-02 1.218282 123.351880 138 310
1169 GO:0060548 1.418872e-03 1.215607 413.634237 460 1034
1170 GO:0006897 2.168634e-02 1.213862 190.114590 212 476
1171 GO:0008610 2.554507e-02 1.212826 178.447427 199 449
1172 GO:0065003 5.121761e-03 1.212438 308.018443 343 785
1173 GO:0051604 4.718813e-02 1.212305 133.611059 149 334
1174 GO:0010243 2.693177e-03 1.211181 371.820808 413 931
1175 GO:0000904 1.505293e-02 1.209817 226.491818 252 568
1176 GO:0030097 3.040849e-03 1.209265 367.630429 408 919
1177 GO:0043434 3.172514e-02 1.209090 168.013907 187 420
1178 GO:0048545 4.838637e-02 1.208974 135.611225 151 339
1179 GO:0045944 1.216537e-03 1.207134 461.451986 511 1156
1180 GO:0042325 4.750102e-03 1.206532 334.403930 371 842
1181 GO:0009306 4.809081e-02 1.205419 140.330242 156 351
1182 GO:0010564 8.537622e-03 1.203012 292.424204 324 731
1183 GO:0045937 4.601032e-03 1.200063 360.029800 398 900
1184 GO:0032989 8.033635e-03 1.200058 306.425363 339 766
1185 GO:0009991 2.750473e-02 1.196265 201.616688 223 504
1186 GO:0061564 3.185070e-02 1.192382 195.616191 216 489
1187 GO:0048812 3.937610e-02 1.182722 193.735680 213 485
1188 GO:0045785 4.594454e-02 1.175939 191.615860 210 479
1189 GO:0042592 1.337900e-03 1.169446 677.656090 736 1694
1190 GO:0071407 3.809682e-02 1.168351 229.942871 251 575
1191 GO:0051172 1.234321e-02 1.168261 368.754839 402 937
1192 GO:0030335 4.503632e-02 1.162081 226.018708 246 565
1193 GO:0009967 5.133116e-03 1.159162 546.613477 592 1373
1194 GO:0001934 3.396615e-02 1.152143 295.624469 320 739
1195 GO:0048585 6.270357e-03 1.144395 628.995111 676 1577
1196 GO:0032879 2.887041e-03 1.139492 846.870095 906 2117
1197 GO:0071345 4.696322e-02 1.137436 302.355298 325 757
1198 GO:0043066 4.411371e-02 1.135020 324.196383 348 812
1199 GO:0048699 1.883655e-02 1.124130 579.247944 617 1448
1200 GO:0007167 4.144985e-02 1.123063 403.233376 430 1008
1201 GO:0050793 1.607510e-02 1.099106 1005.574030 1055 2517
1202 GO:0010468 2.409469e-02 1.070752 1936.990565 1995 4879
Term
1 viral gene expression
2 formation of cytoplasmic translation initiation complex
3 Rap protein signal transduction
4 positive regulation of tumor necrosis factor-mediated signaling pathway
5 pore complex assembly
6 ribosome disassembly
7 nucleoside bisphosphate catabolic process
8 actin filament reorganization
9 purine nucleobase biosynthetic process
10 growth hormone receptor signaling pathway via JAK-STAT
11 histone H3-K36 demethylation
12 cellular response to leucine
13 establishment of endothelial intestinal barrier
14 retrograde transport, vesicle recycling within Golgi
15 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
16 galactose metabolic process
17 Notch receptor processing
18 peripheral nervous system myelin maintenance
19 rescue of stalled ribosome
20 ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
21 regulation of protein export from nucleus
22 termination of RNA polymerase II transcription
23 regulation of synaptic vesicle priming
24 protein import
25 polyadenylation-dependent ncRNA catabolic process
26 plasma membrane to endosome transport
27 establishment of Golgi localization
28 positive regulation of microtubule nucleation
29 modification of postsynaptic actin cytoskeleton
30 regulation of platelet-derived growth factor receptor-beta signaling pathway
31 positive regulation of early endosome to late endosome transport
32 protein localization to cell-cell junction
33 cellular response to arsenic-containing substance
34 antigen processing and presentation of endogenous peptide antigen via MHC class I
35 establishment of protein localization to mitochondrion
36 positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization
37 purine ribonucleoside salvage
38 positive regulation of transcription of Notch receptor target
39 activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c
40 GDP-mannose metabolic process
41 adherens junction maintenance
42 TRIF-dependent toll-like receptor signaling pathway
43 constitutive secretory pathway
44 dAMP metabolic process
45 regulation by virus of viral protein levels in host cell
46 negative regulation of dendritic spine morphogenesis
47 actin polymerization-dependent cell motility
48 nuclear ncRNA surveillance
49 nuclear polyadenylation-dependent rRNA catabolic process
50 nuclear polyadenylation-dependent tRNA catabolic process
51 L-kynurenine metabolic process
52 protein maturation by [4Fe-4S] cluster transfer
53 amyloid-beta clearance by transcytosis
54 positive regulation of autophagosome maturation
55 positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage
56 negative regulation of fatty acid transport
57 negative regulation of epidermal growth factor receptor signaling pathway
58 negative regulation of hippo signaling
59 cellular response to leucine starvation
60 response to type I interferon
61 positive regulation of protein export from nucleus
62 calcium import into the mitochondrion
63 actin filament network formation
64 Golgi lumen acidification
65 long-chain fatty acid import across plasma membrane
66 leucine catabolic process
67 threonine metabolic process
68 N-acetylneuraminate catabolic process
69 transsulfuration
70 hemidesmosome assembly
71 ISG15-protein conjugation
72 low-density lipoprotein receptor particle metabolic process
73 regulation of low-density lipoprotein particle receptor catabolic process
74 positive regulation of toll-like receptor 2 signaling pathway
75 fatty-acyl-CoA catabolic process
76 regulation of pentose-phosphate shunt
77 canonical Wnt signaling pathway involved in regulation of cell proliferation
78 protein import into peroxisome membrane
79 COPI coating of Golgi vesicle
80 protein de-ADP-ribosylation
81 positive regulation of histone H3-K27 methylation
82 parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization
83 lens fiber cell morphogenesis
84 nucleotide-binding oligomerization domain containing 1 signaling pathway
85 aggresome assembly
86 bundle of His cell-Purkinje myocyte adhesion involved in cell communication
87 positive regulation of focal adhesion disassembly
88 succinyl-CoA catabolic process
89 positive regulation of histone deacetylase activity
90 positive regulation of hexokinase activity
91 regulation of endoplasmic reticulum tubular network organization
92 negative regulation of PERK-mediated unfolded protein response
93 positive regulation of protein catabolic process in the vacuole
94 regulation of plasma membrane repair
95 ribosome-associated ubiquitin-dependent protein catabolic process
96 negative regulation of glucocorticoid receptor signaling pathway
97 regulation of caveolin-mediated endocytosis
98 malonyl-CoA metabolic process
99 cytoplasmic translation
100 ubiquinone biosynthetic process
101 inositol phosphate dephosphorylation
102 regulation of Golgi organization
103 translational initiation
104 coenzyme A biosynthetic process
105 MDA-5 signaling pathway
106 glycerol ether biosynthetic process
107 positive regulation of mitochondrial calcium ion concentration
108 commissural neuron axon guidance
109 cellular lipid biosynthetic process
110 lysosomal lumen acidification
111 mitochondrion morphogenesis
112 protein depalmitoylation
113 positive regulation of mitochondrial membrane potential
114 peptidyl-proline hydroxylation to 4-hydroxy-L-proline
115 purine nucleotide salvage
116 transferrin transport
117 endosome to melanosome transport
118 Golgi vesicle budding
119 pigment granule maturation
120 cellular response to lipoteichoic acid
121 positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
122 positive regulation of Arp2/3 complex-mediated actin nucleation
123 positive regulation of interferon-beta production
124 regulation of ubiquitin-protein transferase activity
125 activation of cysteine-type endopeptidase activity
126 GMP biosynthetic process
127 negative regulation of epidermal growth factor-activated receptor activity
128 intraciliary retrograde transport
129 phosphatidylcholine acyl-chain remodeling
130 proton motive force-driven ATP synthesis
131 membrane docking
132 branched-chain amino acid metabolic process
133 virion assembly
134 mannose metabolic process
135 UDP-N-acetylglucosamine biosynthetic process
136 glycerol-3-phosphate metabolic process
137 substrate-dependent cell migration, cell extension
138 positive regulation of sequestering of triglyceride
139 free ubiquitin chain polymerization
140 aminophospholipid transport
141 glycoside catabolic process
142 peroxisome fission
143 negative regulation of cell size
144 positive regulation of centriole replication
145 venous blood vessel morphogenesis
146 nuclear pore complex assembly
147 autophagosome-lysosome fusion
148 cellular response to muramyl dipeptide
149 mitochondrial RNA modification
150 proton motive force-driven mitochondrial ATP synthesis
151 melanosome transport
152 histone H3-K14 acetylation
153 stress-activated MAPK cascade
154 vesicle coating
155 signal peptide processing
156 protein import into peroxisome matrix
157 regulation of nucleotide-binding oligomerization domain containing signaling pathway
158 positive regulation of protein exit from endoplasmic reticulum
159 regulation of endoplasmic reticulum unfolded protein response
160 protein K48-linked ubiquitination
161 respiratory electron transport chain
162 phosphatidylinositol-3-phosphate biosynthetic process
163 response to mitochondrial depolarisation
164 cellular modified amino acid biosynthetic process
165 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
166 positive regulation of type I interferon production
167 regulation of protein targeting to mitochondrion
168 regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
169 positive regulation of macrophage cytokine production
170 establishment of monopolar cell polarity
171 copper ion transport
172 purine deoxyribonucleotide metabolic process
173 melanosome assembly
174 suppression of viral release by host
175 chaperone-mediated autophagy
176 positive regulation of mitochondrial translation
177 RNA surveillance
178 proton-transporting two-sector ATPase complex assembly
179 pentose metabolic process
180 fatty acid beta-oxidation using acyl-CoA dehydrogenase
181 pigment accumulation
182 mitochondrial tRNA processing
183 SRP-dependent cotranslational protein targeting to membrane, translocation
184 signal complex assembly
185 negative regulation of mitochondrial fusion
186 polyamine transport
187 preassembly of GPI anchor in ER membrane
188 post-translational protein targeting to membrane, translocation
189 mitochondrial proton-transporting ATP synthase complex assembly
190 early endosome to Golgi transport
191 B cell chemotaxis
192 embryonic cleavage
193 histone H4-K12 acetylation
194 negative regulation of erythrocyte differentiation
195 viral mRNA export from host cell nucleus
196 type I pneumocyte differentiation
197 positive regulation of necroptotic process
198 centriole elongation
199 microglial cell proliferation
200 proton-transporting V-type ATPase complex assembly
201 tRNA aminoacylation for mitochondrial protein translation
202 regulation of mucus secretion
203 succinate transmembrane transport
204 cellular response to laminar fluid shear stress
205 metanephric nephron tubule morphogenesis
206 response to cell cycle checkpoint signaling
207 response to DNA damage checkpoint signaling
208 stress-induced premature senescence
209 positive regulation of non-motile cilium assembly
210 positive regulation of protein localization to early endosome
211 cellular response to vasopressin
212 positive regulation of xenophagy
213 regulation of pro-B cell differentiation
214 positive regulation of transcription from RNA polymerase II promoter in response to stress
215 regulation of tubulin deacetylation
216 modification of synaptic structure
217 deoxyribonucleotide biosynthetic process
218 protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
219 apical protein localization
220 deoxyribose phosphate biosynthetic process
221 short-chain fatty acid metabolic process
222 peptidyl-lysine acetylation
223 regulation of protein neddylation
224 regulation of mRNA 3'-end processing
225 response to muramyl dipeptide
226 regulation of plasma membrane organization
227 protein deneddylation
228 acetyl-CoA biosynthetic process from pyruvate
229 error-prone translesion synthesis
230 purine nucleoside biosynthetic process
231 ribonucleoside biosynthetic process
232 regulation of ligase activity
233 histone mRNA catabolic process
234 positive regulation of podosome assembly
235 interleukin-17-mediated signaling pathway
236 regulation of mRNA polyadenylation
237 regulation of apoptotic DNA fragmentation
238 regulation of protein lipidation
239 negative regulation of cAMP-dependent protein kinase activity
240 mitochondrial electron transport, NADH to ubiquinone
241 regulation of protein-containing complex disassembly
242 positive regulation of lamellipodium assembly
243 regulation of interferon-beta production
244 NADPH regeneration
245 peptidyl-threonine dephosphorylation
246 establishment of protein localization to peroxisome
247 lysosomal protein catabolic process
248 protein deglycosylation
249 carbohydrate phosphorylation
250 protein K63-linked ubiquitination
251 lysosomal transport
252 cytoplasmic pattern recognition receptor signaling pathway
253 positive regulation of intracellular protein transport
254 mitochondrial fusion
255 negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
256 positive regulation of mitochondrial fission
257 mitochondrial DNA replication
258 cerebellar Purkinje cell layer formation
259 histone H3-K9 demethylation
260 positive regulation of MHC class II biosynthetic process
261 positive regulation of viral entry into host cell
262 semaphorin-plexin signaling pathway involved in axon guidance
263 cellular pigmentation
264 antigen processing and presentation of endogenous antigen
265 establishment of pigment granule localization
266 platelet dense granule organization
267 Arp2/3 complex-mediated actin nucleation
268 establishment of epithelial cell polarity
269 pseudopodium organization
270 fucosylation
271 histone H3-K9 trimethylation
272 establishment of epithelial cell apical/basal polarity
273 protein hydroxylation
274 polyol catabolic process
275 Golgi to plasma membrane transport
276 cortical actin cytoskeleton organization
277 membrane protein ectodomain proteolysis
278 protein localization to Golgi apparatus
279 positive regulation by host of viral process
280 negative regulation of type I interferon-mediated signaling pathway
281 mitochondrial outer membrane permeabilization
282 mitochondrial respiratory chain complex I assembly
283 positive regulation of stress fiber assembly
284 GMP metabolic process
285 nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway
286 peptide antigen assembly with MHC class II protein complex
287 mitochondrial electron transport, ubiquinol to cytochrome c
288 cobalamin metabolic process
289 positive regulation of pseudopodium assembly
290 protein insertion into mitochondrial outer membrane
291 smoothened signaling pathway involved in dorsal/ventral neural tube patterning
292 histone H3 deacetylation
293 negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway
294 regulation of mitophagy
295 positive regulation of autophagy of mitochondrion
296 regulation of RNA binding
297 lactation
298 positive regulation of establishment of protein localization
299 establishment of mitochondrion localization
300 positive regulation of ubiquitin-dependent protein catabolic process
301 regulation of membrane permeability
302 vesicle targeting, to, from or within Golgi
303 protein localization to centrosome
304 cellular copper ion homeostasis
305 RIG-I signaling pathway
306 regulation of fatty acid beta-oxidation
307 negative regulation of translational initiation
308 lipid import into cell
309 phosphorus metabolic process
310 Rac protein signal transduction
311 purine nucleoside monophosphate biosynthetic process
312 histone H2A monoubiquitination
313 peroxisomal transport
314 positive regulation of response to endoplasmic reticulum stress
315 peroxisome organization
316 COPII vesicle coating
317 regulation of establishment of cell polarity
318 negative regulation of protein ubiquitination
319 protein quality control for misfolded or incompletely synthesized proteins
320 receptor catabolic process
321 regulation of cytoplasmic transport
322 hippo signaling
323 purine ribonucleoside triphosphate biosynthetic process
324 TOR signaling
325 endosome transport via multivesicular body sorting pathway
326 organelle localization
327 Golgi vesicle transport
328 stress fiber assembly
329 organelle localization by membrane tethering
330 cellular response to amino acid starvation
331 amino acid activation
332 acetyl-CoA metabolic process
333 cotranslational protein targeting to membrane
334 regulation of mitochondrial gene expression
335 regulation of oxidative stress-induced neuron death
336 ribosomal large subunit assembly
337 negative regulation of defense response to virus
338 negative regulation of keratinocyte proliferation
339 protein localization to endosome
340 negative regulation of release of cytochrome c from mitochondria
341 translational termination
342 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
343 response to sterol depletion
344 activation of NF-kappaB-inducing kinase activity
345 small regulatory ncRNA 3'-end processing
346 cellular response to exogenous dsRNA
347 lamellipodium morphogenesis
348 regulation of chemokine (C-X-C motif) ligand 2 production
349 negative regulation of anoikis
350 glutathione biosynthetic process
351 positive regulation of triglyceride biosynthetic process
352 SREBP signaling pathway
353 negative regulation of tyrosine phosphorylation of STAT protein
354 cytoplasmic sequestering of transcription factor
355 glycosphingolipid catabolic process
356 Golgi inheritance
357 protein heterotetramerization
358 negative regulation of androgen receptor signaling pathway
359 peptidyl-serine dephosphorylation
360 tRNA 5'-end processing
361 positive regulation of ruffle assembly
362 positive regulation of telomerase RNA localization to Cajal body
363 positive regulation of I-kappaB kinase/NF-kappaB signaling
364 positive regulation of autophagy
365 ATP synthesis coupled electron transport
366 epidermal growth factor receptor signaling pathway
367 mitochondrial outer membrane permeabilization involved in programmed cell death
368 negative regulation of response to endoplasmic reticulum stress
369 protein localization to microtubule cytoskeleton
370 endosome organization
371 positive regulation of ubiquitin-protein transferase activity
372 mitochondrial translation
373 endosomal transport
374 peripheral nervous system axon ensheathment
375 monoubiquitinated histone H2A deubiquitination
376 regulation of cytoplasmic translation
377 viral budding
378 mitochondrion transport along microtubule
379 mitophagy
380 negative regulation of histone methylation
381 SNARE complex assembly
382 extracellular vesicle biogenesis
383 protein monoubiquitination
384 ATP metabolic process
385 regulation of ERBB signaling pathway
386 nucleoside triphosphate biosynthetic process
387 Golgi to plasma membrane protein transport
388 integrated stress response signaling
389 tRNA wobble base modification
390 glycerol metabolic process
391 N-glycan processing
392 exosomal secretion
393 nuclear-transcribed mRNA catabolic process
394 regulation of protein targeting
395 anoikis
396 positive regulation of telomere maintenance via telomerase
397 monoubiquitinated protein deubiquitination
398 MHC protein complex assembly
399 oligopeptide transport
400 protein O-linked mannosylation
401 intraciliary anterograde transport
402 protein alpha-1,2-demannosylation
403 regulation of DNA strand elongation
404 establishment of protein localization to telomere
405 epithelial cell-cell adhesion
406 negative regulation of cilium assembly
407 regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
408 mitochondrial genome maintenance
409 viral protein processing
410 multivesicular body assembly
411 positive regulation of pattern recognition receptor signaling pathway
412 ribosome biogenesis
413 protein targeting to lysosome
414 positive regulation of protein targeting to membrane
415 regulation of actin nucleation
416 intra-Golgi vesicle-mediated transport
417 cellular response to growth hormone stimulus
418 late endosome to vacuole transport
419 intracellular lipid transport
420 cellular response to osmotic stress
421 mitochondrial transmembrane transport
422 establishment of protein localization to plasma membrane
423 early endosome to late endosome transport
424 purine nucleoside monophosphate metabolic process
425 pinocytosis
426 regulation of nuclease activity
427 myelin assembly
428 microtubule nucleation
429 lysosome organization
430 iron-sulfur cluster assembly
431 magnesium ion transport
432 protein localization to microtubule
433 DNA damage response, signal transduction resulting in transcription
434 anterograde synaptic vesicle transport
435 positive regulation of type I interferon-mediated signaling pathway
436 RNA localization to Cajal body
437 telomerase RNA localization
438 synaptic vesicle cytoskeletal transport
439 regulation of lamellipodium organization
440 cleavage involved in rRNA processing
441 negative regulation of microtubule depolymerization
442 antigen processing and presentation of exogenous peptide antigen via MHC class II
443 cerebellar Purkinje cell layer development
444 cytoplasmic microtubule organization
445 positive regulation of exocytosis
446 negative regulation of GTPase activity
447 autophagosome maturation
448 negative regulation of TOR signaling
449 positive regulation of protein localization to plasma membrane
450 positive regulation of telomere maintenance
451 aerobic respiration
452 cellular response to topologically incorrect protein
453 protein autoubiquitination
454 movement in host
455 mitochondrial transport
456 ER-nucleus signaling pathway
457 protein destabilization
458 inner mitochondrial membrane organization
459 pigment granule organization
460 Schwann cell development
461 placenta blood vessel development
462 positive regulation of protein targeting to mitochondrion
463 MyD88-dependent toll-like receptor signaling pathway
464 microvillus organization
465 regulation of membrane protein ectodomain proteolysis
466 positive regulation of actin filament polymerization
467 cellular response to ionizing radiation
468 histone deubiquitination
469 regulation of DNA-templated transcription in response to stress
470 regulation of autophagosome assembly
471 regulation of mitochondrial membrane potential
472 tRNA aminoacylation for protein translation
473 histone demethylation
474 intracellular cholesterol transport
475 neural tube closure
476 JNK cascade
477 positive regulation of protein metabolic process
478 NADP metabolic process
479 vesicle docking
480 regulation of transcription involved in G1/S transition of mitotic cell cycle
481 mitochondrial electron transport, cytochrome c to oxygen
482 aspartate family amino acid biosynthetic process
483 regulation of ARF protein signal transduction
484 positive regulation of vacuole organization
485 positive regulation of glycolytic process
486 actin filament bundle assembly
487 selective autophagy
488 regulation of actin filament organization
489 positive regulation of macroautophagy
490 purine nucleoside triphosphate metabolic process
491 purine nucleotide catabolic process
492 nucleoside bisphosphate biosynthetic process
493 positive regulation of proteolysis involved in protein catabolic process
494 regulation of glycolytic process
495 negative regulation of JNK cascade
496 DNA catabolic process, endonucleolytic
497 microtubule anchoring
498 positive regulation of focal adhesion assembly
499 regulation of mitochondrion organization
500 negative regulation of innate immune response
501 non-motile cilium assembly
502 ruffle assembly
503 Wnt signaling pathway
504 cell redox homeostasis
505 vacuole organization
506 protein transport
507 regulation of cell-substrate junction organization
508 ribosomal small subunit biogenesis
509 endoplasmic reticulum to Golgi vesicle-mediated transport
510 positive regulation of interferon-alpha production
511 negative regulation of Rho protein signal transduction
512 sphingoid metabolic process
513 cellular response to misfolded protein
514 negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator
515 negative regulation of membrane permeability
516 histone ubiquitination
517 negative regulation of stress-activated protein kinase signaling cascade
518 mRNA polyadenylation
519 dosage compensation by inactivation of X chromosome
520 regulation of lipopolysaccharide-mediated signaling pathway
521 stress granule assembly
522 regulation of nucleotide-excision repair
523 regulation of double-strand break repair via nonhomologous end joining
524 vesicle targeting
525 necrotic cell death
526 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
527 regulation of focal adhesion assembly
528 protein K63-linked deubiquitination
529 cellular response to epidermal growth factor stimulus
530 neural tube formation
531 regulation of translational initiation
532 pyridine nucleotide metabolic process
533 retrograde transport, endosome to Golgi
534 mitochondrion disassembly
535 regulation of cell shape
536 cellular response to DNA damage stimulus
537 phospholipid biosynthetic process
538 monosaccharide biosynthetic process
539 ribosomal large subunit biogenesis
540 phosphatidylinositol phosphate biosynthetic process
541 gluconeogenesis
542 regulation of tumor necrosis factor-mediated signaling pathway
543 positive regulation of response to cytokine stimulus
544 antigen processing and presentation of peptide antigen
545 myeloid leukocyte cytokine production
546 regulation of extrinsic apoptotic signaling pathway via death domain receptors
547 positive regulation of DNA replication
548 regulation of programmed necrotic cell death
549 protein K48-linked deubiquitination
550 heme biosynthetic process
551 interleukin-1-mediated signaling pathway
552 cellular response to gamma radiation
553 ribonucleoside triphosphate metabolic process
554 phosphatidylserine metabolic process
555 ether metabolic process
556 positive regulation of natural killer cell activation
557 negative regulation of T cell receptor signaling pathway
558 regulation of GTPase activity
559 intracellular transport
560 regulation of protein modification by small protein conjugation or removal
561 cellular response to heat
562 regulation of small GTPase mediated signal transduction
563 cellular nitrogen compound biosynthetic process
564 positive regulation of membrane permeability
565 positive regulation of cell projection organization
566 regulation of centrosome duplication
567 response to antibiotic
568 intracellular protein transport
569 regulation of mitotic spindle organization
570 mRNA catabolic process
571 establishment of protein localization to mitochondrial membrane
572 mitochondrial gene expression
573 protein dealkylation
574 lipid droplet organization
575 phosphatidylinositol dephosphorylation
576 centrosome localization
577 positive regulation of translation
578 intracellular protein transmembrane transport
579 regulation of microtubule polymerization
580 intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
581 B cell apoptotic process
582 telomere maintenance in response to DNA damage
583 positive regulation of release of cytochrome c from mitochondria
584 positive regulation of NF-kappaB transcription factor activity
585 acylglycerol biosynthetic process
586 regulation of mitochondrial membrane permeability involved in apoptotic process
587 positive regulation of substrate adhesion-dependent cell spreading
588 positive regulation of protein polymerization
589 ribose phosphate biosynthetic process
590 nuclear export
591 quinone metabolic process
592 tumor necrosis factor-mediated signaling pathway
593 positive regulation of apoptotic signaling pathway
594 intrinsic apoptotic signaling pathway
595 negative regulation of I-kappaB kinase/NF-kappaB signaling
596 tetrapyrrole biosynthetic process
597 transport along microtubule
598 positive regulation of protein catabolic process
599 RNA splicing
600 antigen processing and presentation of exogenous antigen
601 carbohydrate catabolic process
602 cellular component disassembly involved in execution phase of apoptosis
603 protein K11-linked ubiquitination
604 purine ribonucleotide biosynthetic process
605 regulation of intracellular transport
606 regulation of gluconeogenesis
607 protein targeting
608 protein localization to nucleus
609 dendritic spine development
610 epithelial tube formation
611 alpha-amino acid biosynthetic process
612 protein modification by small protein conjugation
613 maintenance of protein localization in organelle
614 positive regulation of microtubule polymerization or depolymerization
615 regulation of protein stability
616 cellular macromolecule biosynthetic process
617 macroautophagy
618 establishment or maintenance of apical/basal cell polarity
619 protein localization to plasma membrane
620 positive regulation of supramolecular fiber organization
621 membrane fission
622 glycoprotein catabolic process
623 diol metabolic process
624 regulation of filopodium assembly
625 modification-dependent macromolecule catabolic process
626 small GTPase mediated signal transduction
627 positive regulation of cytoskeleton organization
628 ubiquitin-dependent protein catabolic process
629 cytochrome complex assembly
630 dephosphorylation
631 phosphorylation
632 proteasome-mediated ubiquitin-dependent protein catabolic process
633 fatty acid beta-oxidation
634 regulation of protein-containing complex assembly
635 vesicle docking involved in exocytosis
636 circadian regulation of gene expression
637 purine ribonucleoside diphosphate metabolic process
638 nucleobase-containing compound biosynthetic process
639 apoptotic mitochondrial changes
640 response to unfolded protein
641 negative regulation of protein kinase activity
642 phosphatidic acid biosynthetic process
643 positive regulation of transforming growth factor beta receptor signaling pathway
644 cellular response to mechanical stimulus
645 mRNA transport
646 protein localization
647 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
648 positive regulation of catabolic process
649 regulation of dendritic spine development
650 monosaccharide metabolic process
651 G1/S transition of mitotic cell cycle
652 heterocycle biosynthetic process
653 protein targeting to mitochondrion
654 regulation of plasma membrane bounded cell projection assembly
655 activation of cysteine-type endopeptidase activity involved in apoptotic process
656 ATP generation from ADP
657 endocytic recycling
658 positive regulation of glucose metabolic process
659 hexose catabolic process
660 negative regulation of macroautophagy
661 deoxyribonucleotide catabolic process
662 viral release from host cell
663 entrainment of circadian clock by photoperiod
664 deoxyribose phosphate catabolic process
665 lung cell differentiation
666 myelination
667 autophagy
668 ensheathment of neurons
669 histone H4 acetylation
670 cytosolic transport
671 peptide biosynthetic process
672 cellular carbohydrate metabolic process
673 positive regulation of protein modification process
674 regulation of histone deacetylation
675 cellular carbohydrate catabolic process
676 positive regulation of glucose import
677 membrane lipid catabolic process
678 mitochondrial membrane organization
679 proteolysis involved in protein catabolic process
680 transcription elongation by RNA polymerase II promoter
681 isoprenoid biosynthetic process
682 cellular metabolic compound salvage
683 positive regulation of signal transduction by p53 class mediator
684 protein stabilization
685 rRNA metabolic process
686 vesicle localization
687 regulation of macroautophagy
688 mitochondrial respiratory chain complex assembly
689 nucleotide phosphorylation
690 regulation of intrinsic apoptotic signaling pathway
691 positive regulation of cytokine production involved in immune response
692 nucleotide-excision repair
693 telomere capping
694 regulation of reactive oxygen species metabolic process
695 DNA-templated transcription elongation
696 positive regulation of viral process
697 axonal transport
698 androgen receptor signaling pathway
699 cellular response to oxidative stress
700 ribonucleotide catabolic process
701 regulation of myelination
702 thymus development
703 regulation of cell cycle checkpoint
704 cell-substrate junction assembly
705 protein deacylation
706 endosome to lysosome transport
707 regulation of stress fiber assembly
708 purine-containing compound biosynthetic process
709 regulation of biosynthetic process
710 regulation of protein localization to cell surface
711 energy derivation by oxidation of organic compounds
712 monocarboxylic acid catabolic process
713 regulation of protein localization to cell periphery
714 myeloid cell homeostasis
715 cellular macromolecule catabolic process
716 peptidyl-cysteine modification
717 protein modification by small protein removal
718 ribonucleoside monophosphate metabolic process
719 telomere maintenance via telomerase
720 activation of GTPase activity
721 nucleobase metabolic process
722 cerebellar cortex morphogenesis
723 negative regulation of type I interferon production
724 response to fluid shear stress
725 positive regulation of erythrocyte differentiation
726 positive regulation of telomerase activity
727 proton transmembrane transport
728 establishment of protein localization to vacuole
729 regulation of DNA-templated transcription elongation
730 positive regulation of JUN kinase activity
731 organelle fusion
732 regulation of telomere maintenance via telomere lengthening
733 pyruvate metabolic process
734 Golgi organization
735 regulation of cell morphogenesis
736 negative regulation of transferase activity
737 establishment of protein localization to organelle
738 negative regulation of protein-containing complex disassembly
739 regulation of intracellular steroid hormone receptor signaling pathway
740 protein sumoylation
741 cellular response to glucose starvation
742 vesicle transport along microtubule
743 acyl-CoA biosynthetic process
744 lens fiber cell differentiation
745 cellular response to cadmium ion
746 rRNA processing
747 protein autophosphorylation
748 peptidyl-serine phosphorylation
749 endothelial cell development
750 endoplasmic reticulum unfolded protein response
751 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
752 positive regulation of stem cell population maintenance
753 nucleotide transport
754 positive regulation of epidermal growth factor receptor signaling pathway
755 positive regulation of protein-containing complex assembly
756 positive regulation of double-strand break repair
757 ribonucleotide metabolic process
758 protein homotetramerization
759 positive regulation of axonogenesis
760 positive regulation of protein dephosphorylation
761 developmental pigmentation
762 actin cytoskeleton reorganization
763 nucleocytoplasmic transport
764 dendritic spine organization
765 glycerophospholipid biosynthetic process
766 mRNA stabilization
767 DNA synthesis involved in DNA repair
768 regulation of fibroblast migration
769 positive regulation of protein import into nucleus
770 toxin transport
771 post-translational protein modification
772 regulation of RNA splicing
773 viral transcription
774 I-kappaB kinase/NF-kappaB signaling
775 cellular response to hydrogen peroxide
776 clathrin-dependent endocytosis
777 regulation of cellular response to stress
778 cellular response to insulin stimulus
779 toll-like receptor 4 signaling pathway
780 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
781 transcription by RNA polymerase III
782 maturation of SSU-rRNA
783 negative regulation of actin filament polymerization
784 establishment of RNA localization
785 regulation of protein localization
786 post-Golgi vesicle-mediated transport
787 peptidyl-threonine phosphorylation
788 lamellipodium assembly
789 regulation of cell morphogenesis involved in differentiation
790 cellular response to type I interferon
791 protein targeting to ER
792 semaphorin-plexin signaling pathway
793 nucleic acid transport
794 localization within membrane
795 lipid oxidation
796 establishment or maintenance of cell polarity
797 histone deacetylation
798 establishment of protein localization to membrane
799 actin filament polymerization
800 purine nucleotide metabolic process
801 glucose metabolic process
802 centriole assembly
803 positive regulation of reactive oxygen species metabolic process
804 negative regulation of protein-containing complex assembly
805 thioester metabolic process
806 tRNA metabolic process
807 ceramide metabolic process
808 regulation of protein localization to membrane
809 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
810 positive regulation of TOR signaling
811 regulation of cellular respiration
812 regulation of TORC1 signaling
813 response to starvation
814 centrosome cycle
815 cellular response to nutrient levels
816 cellular metabolic process
817 protein import into nucleus
818 cellular oxidant detoxification
819 nucleotide biosynthetic process
820 regulation of proteasomal protein catabolic process
821 intermembrane lipid transfer
822 positive regulation of extrinsic apoptotic signaling pathway
823 bone resorption
824 ncRNA transcription
825 cellular response to acid chemical
826 negative regulation of protein modification process
827 porphyrin-containing compound metabolic process
828 nucleobase-containing small molecule metabolic process
829 regulation of autophagy
830 substrate adhesion-dependent cell spreading
831 macromolecule localization
832 nucleoside phosphate metabolic process
833 intracellular estrogen receptor signaling pathway
834 regulation of cysteine-type endopeptidase activity involved in apoptotic process
835 modulation by host of symbiont process
836 regulation of actin polymerization or depolymerization
837 regulation of cytoskeleton organization
838 erythrocyte differentiation
839 nucleobase-containing compound catabolic process
840 ubiquitin-dependent ERAD pathway
841 nucleoside diphosphate metabolic process
842 microtubule polymerization or depolymerization
843 protein dephosphorylation
844 actin filament depolymerization
845 regulation of DNA repair
846 cellular biosynthetic process
847 regulation of actin filament-based process
848 protein localization to endoplasmic reticulum
849 regulation of p38MAPK cascade
850 endoplasmic reticulum organization
851 regulation of cellular catabolic process
852 negative regulation of cold-induced thermogenesis
853 ribonucleoprotein complex subunit organization
854 negative regulation of RNA catabolic process
855 positive regulation of transcription elongation by RNA polymerase II
856 negative regulation of reactive oxygen species metabolic process
857 morphogenesis of embryonic epithelium
858 steroid hormone mediated signaling pathway
859 negative regulation of protein serine/threonine kinase activity
860 organic acid catabolic process
861 positive regulation of response to DNA damage stimulus
862 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
863 regulation of lipid kinase activity
864 mammary gland epithelium development
865 positive regulation of regulated secretory pathway
866 regulation of protein depolymerization
867 positive regulation of protein localization
868 catabolic process
869 nucleoside phosphate catabolic process
870 cellular response to external stimulus
871 regulation of response to cytokine stimulus
872 response to ischemia
873 regulation of microtubule cytoskeleton organization
874 positive regulation of T cell mediated immunity
875 negative regulation of viral genome replication
876 T cell apoptotic process
877 extrinsic apoptotic signaling pathway
878 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
879 carbohydrate derivative transport
880 cellular response to toxic substance
881 insulin secretion involved in cellular response to glucose stimulus
882 negative regulation of intrinsic apoptotic signaling pathway
883 response to tumor necrosis factor
884 reactive nitrogen species metabolic process
885 protein-containing complex disassembly
886 ribonucleoside bisphosphate metabolic process
887 purine nucleoside bisphosphate metabolic process
888 signal transduction by p53 class mediator
889 mitotic cytokinesis
890 response to reactive oxygen species
891 positive regulation of DNA-templated transcription
892 positive regulation of NIK/NF-kappaB signaling
893 Rho protein signal transduction
894 regulation of purine nucleotide metabolic process
895 chaperone-mediated protein folding
896 regulation of cellular response to oxidative stress
897 negative regulation of cytoskeleton organization
898 protein O-linked glycosylation
899 positive regulation of macromolecule biosynthetic process
900 spindle assembly
901 nitric oxide biosynthetic process
902 regulation of organelle assembly
903 mitochondrion organization
904 negative regulation of phosphorylation
905 regulation of protein polymerization
906 alternative mRNA splicing, via spliceosome
907 regulation of Ras protein signal transduction
908 histone H3 acetylation
909 myeloid cell development
910 DNA damage response, signal transduction by p53 class mediator
911 sulfur compound transport
912 positive regulation of protein binding
913 cellular lipid catabolic process
914 lipid storage
915 regulation of cell cycle
916 organic substance biosynthetic process
917 platelet-derived growth factor receptor signaling pathway
918 negative regulation of small GTPase mediated signal transduction
919 phosphate-containing compound metabolic process
920 negative regulation of MAP kinase activity
921 positive regulation of organelle organization
922 phosphatidylinositol metabolic process
923 cellular response to stress
924 negative regulation of mRNA metabolic process
925 autophagosome assembly
926 negative regulation of intracellular transport
927 ribonucleoprotein complex biogenesis
928 regulation of protein localization to nucleus
929 membrane fusion
930 protein acylation
931 organophosphate catabolic process
932 cellular amide metabolic process
933 integrin-mediated signaling pathway
934 negative regulation of cellular catabolic process
935 insulin receptor signaling pathway
936 regulation of cellular component size
937 mRNA metabolic process
938 cellular response to oxygen levels
939 positive regulation of protein ubiquitination
940 lysosome localization
941 organophosphate metabolic process
942 positive regulation of proteolysis
943 regulation of cell projection organization
944 maintenance of protein location
945 cell cycle phase transition
946 response to endoplasmic reticulum stress
947 protein modification process
948 actin filament organization
949 regulation of protein binding
950 regulation of mRNA stability
951 macromolecule biosynthetic process
952 regulation of chromosome organization
953 internal peptidyl-lysine acetylation
954 stem cell population maintenance
955 sulfur compound biosynthetic process
956 protein localization to organelle
957 transition metal ion homeostasis
958 regulation of nucleocytoplasmic transport
959 viral genome replication
960 negative regulation of response to DNA damage stimulus
961 regulation of toll-like receptor signaling pathway
962 positive regulation of endopeptidase activity
963 protein-containing complex localization
964 glycosylation
965 negative regulation of phosphorus metabolic process
966 carbohydrate derivative metabolic process
967 glycolipid metabolic process
968 cellular response to ketone
969 RNA destabilization
970 protein ubiquitination
971 protein phosphorylation
972 membrane lipid metabolic process
973 vesicle fusion
974 negative regulation of cell projection organization
975 regulation of cellular component biogenesis
976 RNA 3'